Government Agency of Fiction

"INS Agent: You ever heard of Division 6? Police Officer: There is no Division 6. This is bullshit. INS Agent: Yeah."

- Men in Black

This trope covers two kinds of government agency, those that are entirely fictional, and current genuine agencies described in a fictional way.

They are often shown in the same way, either as obstructive bureaucrats, or the Government Conspiracy. Many of these will only be seen as the organisation behind our heroes, paying their wages and Hero Insurance and assigning them missions (such as the first few on this list), providing occasional back-up (such as SHIELD in the Marvel Universe), or hunting for our unusual heroes (because they're aliens secretly operating on Earth, say). Sometimes, they'll just be inventing silly walks.

This organization may employ The Men in Black.

Compare Heroes-R-Us, Law Enforcement, Inc.. Government Agencies of Fiction sometimes have Fun with Acronyms.

Anime and Manga

 * The Worlds Welfare Work Association (3WA), with troublesome agents Kei and Yuri (Dirty Pair).
 * Public Security Section 9 in the Ghost in the Shell franchise, as well as the Cabinet Intelligence Agency in Stand Alone Complex 2nd GIG.
 * They were intended to be more like fictional branches of the very real (although less than widely publicised) Japanese intelligence establishment. It isn't a monolithic entity, but is more like an umbrella organisation coordinating various semi-independent sections, so a couple of fictional ones would fit the structure just fine.
 * Hypnos and DATS in Digimon, MIB agencies.
 * The RAPD in Burst Angel.
 * NERV, SEELE and GEHIRN from Neon Genesis Evangelion, although NERV is the one that gets 95% of the screen time.
 * The Social Welfare Agency in Gunslinger Girl.
 * The Organization from Suzumiya Haruhi probably counts too.
 * The Science Patrol in Ultraman.
 * Then, there are the BRAVE HEROES of the Gutsy Galaxy Guard of GaoGaiGar fame. 3G BANZAI!!!
 * And their American and Chinese branches and French sister organization, Chasseur, all with their own contingent of Brave Robots.
 * The Time-Space Administration Bureau of Magical Girl Lyrical Nanoha. Granted, it serves an alien government, but...
 * 'course, in StrikerS the focus is on the Bureau's homeworld, so it isn't quite so alien anymore.
 * The Hentai Spy of Darkness has the Special Security Services Cabinet, which gives the spies of Q-section their marching orders.
 * The Sakura Kikan in Senkou no Night Raid.
 * Heroman includes the NIA (National Intelligence Agency), a domestic surveillance/law enforcement (?) agency that works closely with the military and seems to take its orders directly from the President.

Comics

 * The Marvel Universe has various United Nations agencies: SHIELD (Supreme Headquarters International Espionage Law-enforcement Division/Strategic, Hazard Intervention, Espionage Logistics Directorate.), SWORD (Sentient World Observation and Response Department), and ARMOR (Altered-Reality Monitoring and Operational Response). An evil multinational agency called Operation Zero Tolerance briefly existed to stomp on mutants, and Weapon Plus does the same thing.
 * The United States has HATE (Highest Anti-Terrorism Effort) sometimes, the CSA (Commission of Superhuman Activities), and O*N*E (Office of National Emergency). During the Dark Reign story, SHIELD was replaced by dodgy organisation HAMMER.
 * The United Kingdom has MI13, the metahuman/supernatural/extra terrestrial branch of the Directorate of Military Intelligence (the designation is not used in reality). Previous British agencies were *deep breath*: STRIKE (Special Tactical Reserve for International Key Emergencies, a UK SHIELD), WHO (the Weird Happenings Organisation, a Shout-Out to UNIT), Black Air, RCX (the Resource Contol eXecutive) and DUCK (Yes, really. Department of Unknown and Covert Knowledge). Some of these organisations turned out to be evil, and the exact juristiction boundaries (or even which ones, if any, existed at the same time) were never clearly established. An MI13 story Lampshaded this by having an MI 6 officer remark none of these agencies will ever last.
 * Canada has Department H in the Alpha Flight comics.
 * The 13th Bureau of the Yellow Empire on Blake & Mortimer Comics.
 * The DCU also had a fictional version of the OSS; in the modern era, it has Checkmate (later handed over to the United Nations), Project Cadmus, the DEO (Department of Extra-Normal Operations), the DMA (Department of Metahuman Affairs), SHADE (Super Human Advanced Defense Executive), and the Global Peace Agency.
 * Acclaim Comics had the Domestic Operations Authority, or DOA. Usually the good guys in Turok, not so much in Bloodshot.
 * GUN (Guardian Unit of Nations) and the CIA (Central Information Agency) in the Sonic the Hedgehog series.
 * The Culper Ring in Y: The Last Man. In reality, it was George Washington's spy network. Here they still exist as a "covert arm of the executive branch".
 * This is the entire basis for almost all incarnations of G.I. Joe. They go as far as to fake their members' deaths in the latest comic series.
 * The Marvel mini-series "Pryde and Wisdom", Pete Wisdom and Kitty Pryde work for a police agency called Dept F.66, The Department of Unusual Deaths.
 * Bureau of Paranormal Research and Defense, employers of Hellboy.
 * Transformers comics have had a few, starting with the Intelligence and Information Institute (III) that was meant to handle the Transformers for the US government (i.e. give a fake story about where they came from and refuse to notice the Autobots were goodies). The IDW comics had Skywatch.
 * Madman has Tri-Eye. Its true intentions are pretty vague but they seem to have a hand in everything that happens.

Fan Works

 * "Gemstone", an international organization established to help -- and learn from -- Team RWBY when they're unexpectedly transported to Earth from Remnant in the RWBY fanfic series Emergence.

Film
""Never heard of it." "Never will.""
 * Sector 7, from Transformers.


 * Subverted by The Agency of the Men in Black, AKA the INS (Immigration and Naturalization Service) Division 6. They outright state they do not represent any branch of the government (because that would involve "too much paperwork"). As a result, they are 100% privately funded, though that isn't a problem because they own the patents for Velcro and microwave ovens (which were actually invented by aliens).
 * In the animated version, they identify themselves to civilians as Division 6 of whatever real governmental agency would sound appropriate. So for episode dealing with alien plants, they'd identify themselves as Department of Agriculture, Division 6, an episode dealing with extraterrestrial drugs would have them calling themselves Drug Enforcement Agency, Division, 6, and so on.
 * The Ministry of Information and the Information Retrieval Department from Brazil.
 * The OSS in the Spy Kids trilogy. In reality, it was the predecessor of the CIA and is now defunct. In their world, it is still active.
 * The Central Security Agency from the Jackie Chan film The Tuxedo, which justifies Tuxedo and Martini by manufacturing ultra high-tech spy tuxedos that they issue to their field agents.
 * The Multiverse Authority from The One is basically an inter-dimensional FBI that hunts down and arrests people who kill their counterparts. (It's not all they do, but everything else is on a now-defunct website.)
 * The House Commitee of Racial Identity in CSA: Confederate States of America.
 * Push has the Division, a government agency dedicated to hunting down and training psychics (remote viewers, telekinetics, empaths, etc.) for the purposes of espionage and covert ops. There was, apparently, a Chinese version, which has been disbanded and absorbed by the Triads. The Division bears many similarities to the Psi Corps from Babylon 5 in that they have a hidden agenda, conduct secret research, and attempt to create an army of super-psychics.
 * MI 7 in Johnny English. Possibly unknown to the filmmakers there really was a British Military Intelligence Section 7: it was in charge of propaganda and was eventually extinguished.

Literature
""More and more it had become a crime-fighting agency, a counterespionage system. Into its own hands it was drawing more and more of the threads of government.""
 * Any Ruritania wouldn't be complete without their Zekrett Politzs.
 * The Department Of Metahuman Affairs in Soon I Will Be Invincible.
 * Bureau of Sabotage (BuSab) from Frank Herbert's Con Sentiency series.
 * Jerry Pournelle's CoDominium has a large number of fictional bureaus that deal with various areas as colonization, technology, correction, forced relocation, and even a anti-tech Secret Police.
 * ARM (originally Amalgamated Regional Militia) of Larry Niven's Known Space, basically the UN police force, consisting entirely of paranoid schizophrenics, and quite possibly led by a psychopathic overprotective superintelligent posthuman.
 * The Bureau, the British intelligence agency of the Quiller novels.
 * Stephen King's Department of Scientific Intelligence ("The Shop") in Firestarter and other stories.
 * The Uncle Ira Group and Special Forces Warrant Agency from The War Against the Chtorr—in a future United States which has been demilitarised by force, they serve as the country's (illegal) intelligence and black ops units.
 * CURE, a secret U.S. government agency the The Destroyer book series. It was created by President John F. Kennedy to destroy threats to United States by working outside the U.S. Constitution.
 * The Hardy Boys Casefiles series has the Network, employing the boys' occasional ally Mr. Grey.
 * The Thought Police in 1984.
 * Also the Ministries of Truth, Peace, Love, and Plenty.
 * The Laundry, the UK's Eldritch Abomination response team in Charles Stross novels. Also their American counterparts, the Black Chamber, and their German counterparts, the Geheime Sicherheit Abteilung (Secret Security Department, also known as the "Faust Force").
 * The Black Chamber, for history nerds, is the original version of the NSA.
 * The Council of Science in Isaac Asimov's Lucky Starr series of stories. It started out as an advisory body, but:


 * BioCon corporation worked under the government creating genetic experiments, but one escaped and now the FBI has to chase him.
 * The Ministry of Magic in Harry Potter.
 * All governments in Discworld are obviously fictional, but the only one organised enough to have actual agencies (beyond "a bunch of soldiers hired by the feudal ruler") is Ankh-Morpork. The Dark Clerks seem to be the organisation that deals with situations Vetinari feels might be dangerous, but which it would be inappropriate for the Watch to deal with. They're Assassins' Guild graduates, often scholarship boys (ie. they entered the Guild because they were already really good at killing, not because their family had money).
 * The former Patricians had a Secret Police called the Cable Street Particulars, now reinvented as the Watch's investigative and undercover arm.
 * The Kingdom of Lancre has several governmental agencies, departments and bodies. It's just that they're all run entirely by Shawn Ogg.
 * The Fantasy Counterpart Culture of...Asia...on the Counterweight Continent also has all the formal trappings of imperial China, cradle of bureaucracy, and so presumably has massive numbers of intricately named departments. We just don't meet them, because Rincewind spends all his time running and Cohen spends all his time stabbing people.
 * Of course, in Jasper Fforde's Thursday Next series, there is an actual Government Agency of Fiction, the SO27 LiteraTec division...
 * Kim Newman is one of several writers who've taken Sherlock Holmes's statement that, on occasion, brother Mycroft is the British Government to portray the Diogenes Club as a secret government agency under his control.
 * Michael Gilbert wrote a number of short stories about two middle-aged spies, Mr. Calder and Mr. Behrens, who after twenty-some years each in MI 6 joined another agency, the Joint Services Standing Intelligence Committee's External Branch. "If there's a job which is so disreputable that none of the departments will handle it, we give it to the 'E' Branch."
 * The Anti-Hero of The Eiger Sanction worked for CII ... which isn't initials, it's a Roman numeral referring to the fact that 102 different spy agencies got merged to form this abomination. It's headed by an Evil Albino war criminal named Yurasis Dragon, and there's a strong hint that one of the agency's first tasks was murdering several of the witnesses to his wartime crimes in order to make things safe for him.

Live Action TV

 * Stargate SG-1 had various government organizations that fit more of an Alphabet Soup role, such as the NID (National Intelligence Department), later replaced with the IOA (International Oversight Advisory).
 * NID and IOA, in particular, were created as antagonists. the USAF's Stargate Command, of course, are the protagonists.
 * If Stargate Command doesn't count for this, then it's expanded version in Universe, Homeworld Command certainly does.
 * Star Trek creates several of these. Occasionally mentioned are the Bajoran, Vulcan and Klingon intelligence agencies. However, three do get a more significant exploration:
 * Section 31 (Federation), a black ops agency so secret it doesn't even have a headquarters. Most of the Federation doesn't know exists. Those that do turn a blind eye to its existence.
 * The Tal Shiar (Romulan), as a reputation for being one of the most efficient organisations in the entire Alpha/Beta Quadrants. Not many organisations have a better reputation. It's considered dangerous enough for the Dominion to target for being wiped out as a prelude to invading the Alpha Quadrant.
 * The Obsidian Order (Cardassian), the only organisation with a better reputation for efficiency and success than the Tal Shiar. Like the Tal Shiar, the Dominion views it as such a big threat that it wipes out the Order as a prelude to invading the Alpha Quadrant. The Obsidian Order is eventually replaced by the Cardassian Bureau of Intelligence which also very quickly gains a reputation for skill and efficiency at what it does.
 * UNIT (United Nations Intelligence Taskforce, later the UNified Intelligence Taskforce) in the Whoniverse.
 * CTU (Counter-Terrorist Unit) in 24.
 * CONTROL in Get Smart.
 * The Initiative from Buffy the Vampire Slayer.
 * Power Rangers has Operation Lightspeed, a demon-fighting rescue organization; Time Force, Time Police from the year 3000; and Twenty Minutes Into the Future it will have a Space Police group called Space Patrol Delta. In an undefined place continuity-wise is the sinister Alphabet Soup, a scientific think-tank.
 * The Agency in the Sci-Fi Channel The Invisible Man series. Arguably a parody, as it seems to have only two field agents (three in the second season), one boss with one personal assistant, and one Hot Scientist, and suffers from frequently being transferred to branches of The Government that have nothing to do with intelligence (Dept. of Fish and Game, Bureau of Indian Affairs, Dept. of Health and Human Services, the US Postal Service...)
 * The Equalizer. Robert McCall's former employer is only referred to as "The Agency" or "The Company", both well-known nicknames for the CIA. Not actually calling it the CIA gets around the issue of how the mysterious Agency can legally operate inside the United States, which it does in quite a few episodes.
 * Monty Python's Flying Circus: The Ministry of Silly Walks.
 * The United Network Command for Law and Enforcement—U.N.C.L.E.--of the 60s spy series The Man From UNCLE. U.N.C.L.E. is more of a multi-national, supra-governmental agency than an agency of one government, though (U.N.C.L.E. operatives are drawn from many of the nations of the world, even the (then) Soviet Bloc as well as the Free World, and it seems assumed without explicitly stating that U.N.C.L.E. is funded by various national governments and operates with their blessing and cooperation).
 * The DXS (Department of External Services) in MacGyver.
 * The 4400 has NTAC (National Threat Assessment Command), a division of Homeland Security.
 * The A.R.C. (Anomaly Research Centre) They investigate anomalies and fight dinosaurs, when necessary. And generally cover stuff up with Blatant Lies.
 * M.I. 9 from M.I. High.
 * The NIA (a combination of every scare story about the CIA and NSA) in The Rockford Files, Codename Foxfire, and Lois and Clark.
 * The Academy in Firefly is a government agency that appears to conduct experiments on children to turn them in psychic Super Soldiers.
 * The Hands of Blue, or whoever they work for.
 * CI5, the organised crime, terrorism and spy fighting agency that employs The Professionals.
 * Dempsey and Makepeace has SI10, which fulfils a similar role to CI5, though it has a more rigid hierarchy and appears to be an actual police unit.
 * The AMC series Rubicon has the American Policy Institute, a government think tank that seems to do most of the intelligence gathering for other agencies.
 * Nikita has Division, a black-ops program that doesn't officially exist, and originally reported to a secret group of government officials known as Oversight. However, its leader, Percy, has since gone rogue, and Division now works for the highest bidder. And unfortunately, Percy has taken steps to insure that he can never be removed from power without bringing the entire US government down with him.
 * Gogol is initially presented as the Russian version of Division but Nikita quickly points out that while they employ many former government agents, they have always been just a mercenary organization. They are later revealed to be part of a Russian Mega Corp
 * La Femme Nikita had Section 1, which was one of the many Sections under the control of Oversight, which in turn was under the control of Center.
 * Farscape had IASA (International Aeronautics and Space Administration), an International Agency of Fiction.
 * The Department of Administrative Affairs in Yes Minister. The ultimate government bureaucracy, it's in charge of organising all the other government bureaucracies.
 * Similarly, the Department of Social Affairs and Citizenship (DoSAC) in The Thick of It, created on account of the Prime Minister's preference for "joined-up government" (a sly reference to some of the weirder departments cooked up by Tony Blair and Peter Mandelson).
 * The agents of InSecurity work for NISA, a fictional Canadian agency based partly on the real CSIS (Canadian Security and Intelligence Service.) It's also mostly based on spy agencies as seen on TV.
 * Colonel Steve Austin, The Six Million Dollar Man, was employed by the O.S.I. (Office of Scientific Intelligence).
 * In the 1960's spy show It Takes A Thief, Alexander Mundy was released from jail to perform missions for the U.S. SIA (Secret Intelligence Agency).
 * The Fringe Division in, well, Fringe.
 * The warehouses in the show Warehouse 13 are an interesting example, because they aren't really a real part of the government.
 * Smallville, in addition to Checkmate from the comics, had a thinly-disguised DHS called the Department of Domestic Security.
 * A Reunion Show of The Wild Wild West (TV series) ended with a present-day message from the director of a U.S. agency "so secret that even I don't know the name of it." (It was a warning that Dr. Loveless Junior might have created an atomic bomb the U.S. government never found....)

Tabletop Games

 * Hunter: The Vigil has three—Task Force: VALKYRIE, The Men in Black who came together after hiring an actor to cover up the fact that some thing had eaten President Lincoln; the Barrett Commission, a political coalition that works to keep vampiric influence out of the halls of power; and the Vanguard Serial Crimes Unit, a branch of the FBI trained in Psychic Powers and specializing in the pursuit of slashers.
 * GURPS Transhuman Space mostly uses existing agencies, but the US has the National Technical Intelligence Bureau (futuristic NSA) and the Space Intelligence Agency; the EU has the Genetic Regulatory Agency; and Indonesia (one of the main players in the Transpacific Socialist Alliance) has BAKORSTAPAS. There's even a fictional fictional government agency; S.P.I.D.E.R., who fight the eco-terrorists of K.H.A.O.S. in a series of popular kids shows.
 * Department 7, the all-purpose government agency tasked with investigating whatever the Gamemaster wants them to, from D20 Modern.
 * Bureau 13 in Tri Tac Games' Bureau 13: Stalking the Night Fantastic. They're a top secret U.S. government agency dedicated to defending the world against supernatural threats.
 * The secret, unofficial (and illegal) Delta Green from Call of Cthulhu (tabletop game), which is dedicated to stopping Cthulhu Mythos threats. Its British counterpart is PISCES (Paranormal Intelligence Section for Counter-intelligence, Espionage and Sabotage).
 * Villains and Vigilantes had C.H.E.S.S. (Central Headquarters of Esiponage for the Secret Service), a U.S. government agency that fought super menaces.
 * In Paranoia the Computer had a number of organizations carrying out its orders, such as Armed Forces, CPU and Internal Security.

Video Games

 * The AMS in House of the Dead
 * Also in the film version
 * The Agency, employing cyborgs to bring peace to Pacific City today and the world later, in the XBox's Crackdown.
 * The five nation alliances in Evil Genius: P.A.T.R.I.O.T., S.A.B.E.R., S.M.A.S.H., H.A.M.M.E.R., and A.N.V.I.L.
 * The Agency and its more benign successor, the International Presidential Consulting Agency, from Syphon Filter.
 * Destroy All Humans! has the Majestic
 * The Ministry Of Occultism in the Chzo Mythos.
 * The National Security Executive in Second Sight. Pretentious Latin Motto: Silent Leges Inter Arma.
 * HECU (Hazardous Environment Combat Unit) in the original Half-Life game.
 * The Civil Emergency and Defense Agency (CEDA) in Left 4 Dead.
 * The Conduit has The Trust.
 * And there's Alpha Protocol in the game of the same name.
 * Subverted in Deus Ex, as UNATCO appears to be a legitimate world law-enforcement body
 * Task Force 141 in Modern Warfare 2.
 * Mike Toreno's "government agency" in Grand Theft Auto: San Andreas. Plus at least one (probably two) rival agencies.

Web Comics

 * Code Name: Hunter gives us the Royal Center for Special Investigations.
 * The Templar from Parallel Dementia.
 * The Quad from Spy6teen
 * General Protection Fault has a secret spy agency referred to as UGA, which is short for... Undisclosed Government Agency.

Web Original

 * The dreaded Mutant Commission Office in the Whateley Universe. Mutants often call it the 'Mutant Control Office'.
 * The SCP Foundation features the Unusual Incidents Unit of the FBI, their world's equivalent of "The X-Files".
 * Avelia's Office of Strategic Services and Sirene's Reichsnachrichten from Open Blue.
 * The League of Intergalactic Cosmic Champions operated under the Department of Superheroics.
 * The Fear Mythos features the SMSC and Sgt. Peppers, two organizations dedicated to fighting the Fears.

Western Animation

 * Section 13 - Jackie Chan Adventures.
 * Also, The Venture Brothers' Office of Secret Intelligence. The main branch operates much like SHIELD, but apparently a splinter group is a Captain Ersatz for G.I. Joe.
 * The Dai Li from Avatar: The Last Airbender
 * Global Justice, an international crimefighting agency who sometimes call on Kim Possible.
 * Danny Phantom has The Guys in White, a governmental agency dedicated to ghostly research/hunts.
 * Phineas and Ferb has the O.W.C.A. (Organization Without a Cool Acronym), which employs Animal Secret Agents to fight Mad Scientists.
 * ISIS and ODIN in Archer
 * Jonny Quest. In the original series Race Bannon worked for a U.S. Government organization called Intelligence One and Dr. Quest sometimes helped them out. It only appeared in two episodes, "The Mystery of the Lizard Men" and "Riddle of the Gold".
 * The Iron Giant. Mansley mentions that he "works for the government" when he flashes his badge for the "BUP."

Anime and Manga

 * The FBI is a consistent presence in Death Note, although why they are suddenly investigating international cases instead of the CIA is never explained.
 * Interpol of Lupin III, through the tenacious Zenigata
 * The NPA is mentioned at least once in You're Under Arrest, being the coordinating agency for police forces.

Comics

 * Queen and Country started out referring to British domestic intelligence as "Five" (like The Sandbaggers does,) but Greg Rucka was embarrassed to discover that most people nowadays refer to the agency as "Box", a nickname derived from the agency's official address, a PO Box. He promptly corrected the error in the rest of the series.
 * William Gravel (think Constantine meets Jack Bauer), protagonist of various Warren Ellis' comics, is a Sergeant Major in the SAS (Special Air Service).
 * In Sluggy Freelance the FBI operated the Orsintos Labs project that studied various paranormal phenomena, including Oasis. It's explained that they did this because they were jealous the CIA hogging all the alien cases.
 * In Marvel Comics, the real-life MI 5, MI 6 and the Joint Intelligence Committee have all appeared in MI 13 stories written by Paul Cornell. MI 6 previously ran superhero operations in Shang Chi, Master of Kung Fu.
 * The Boys are backed by the CIA.
 * The MI 5 and MI 6 in The League of Extraordinary Gentlemen, where not only works every British spy and agent from fiction (from John Drake, James Bond, Emma Peel and more), but it was also used as The Ministry Of Love.

Film

 * INS (Immigration and Naturalization Service) Division 6, one of J's cover stories in Men in Black.
 * After its absorption into Department of Homeland Security, however, it was reorganized into Customs and Border Protection on border control, and US Citizenship and Immigration Service for immigration.
 * MI6, as seen in James Bond.
 * Referred as simply the British Secret Service in the Fleming novels.
 * Ditto SMERSH, before their role was usurped by the completely-fictional S.P.E.C.T.R.E..
 * Die Another Day also includes the NSA.
 * The characters in The Mentalist work for the CBI (California Bureau of Investigation).
 * Department of Defense in Eagle Eye
 * The Nuclear Emergency Support Team appears in Transformers: Revenge of the Fallen as... let's just let the TFWiki try to explain it.
 * Buckaroo Banzai. The Secretary of the U.S. Department of Defense is a pain in Buckaroo's neck. He badmouths Buckarooo to other people and tries to convince the President to confiscate Buckaroo's Jet Car.
 * In Sneakers the NSA is behind the project to develop the little black box and ends up hunting the protagonists after they steal it.
 * The NSA started a program to recruit XXX.

Literature

 * MI6 was also seen in John Le Carre's works. It's nicknamed "The Circus" thanks to its headquarters being on Cambridge Circus (in-universe; in real life MI6 headquarters overlooks the Thames).
 * It is called the Circus until sometime between the end of Smiley's People and the start of The Russia House, when the main part of the Service, as it then becomes known, moves to an unpleasant office building on the south bank of the Thames, which is stated more clearly in The Secret Pilgrim. This is explained as being partly because of a desire to get rid of everything which reminds them of The Mole from Tinker Tailor Soldier Spy, especially because they know he bugged the Circus before he was caught.
 * NUMA, the National Underwater and Marine Agency, a federal institution out of the Dirk Pitt novels by Clive Cussler led to the founding of a private organization of the same name which is headed by the author.
 * The Beeks in Child of the Hive are a government organisation officially known as DPNI: Department for the Protection of National Intellect.
 * The FBI is after Fox Tayle because he escaped from the fictional governmental Bio Con corporation.
 * SMERSH figured heavily in the James Bond novels by Ian Fleming (at least till use of the organization was phased out around the time of Thunderball). However, the organization was never the super spy organization depicted, and may not have been in existence by the time that the Bond novels debuted. SMERSH (from SMERt SHpionam, or "death to spies") was in reality a sub-branch of the NKVD/MGB that was tasked during (The Great Patriotic War) with ferreting out ant-communist partisans, Nazi sympathizers and other enemies of the Soviet regime behind Soviet lines. They were also put in charge of the short manhunt for Adolf Hitler in Berlin at the end of the war. SMERSH was offically closed down in March 1946.

Live Action TV

 * Chuck is press-ganged into working for both the CIA and NSA.
 * The British Security Service (MI5) is depicted in Spooks.
 * NCIS, CGIS and Mossad from NCIS, though an incredible amount of people in the show haven't heard of it... which is justified because most people only know about the organisation because of the show.
 * More realistic takes on MI6 (although referred to as SIS, its real name) and MI5 can be found in The Sandbaggers and Queen and Country (although both depict SIS using a structure reportedly closer to the real CIA.)
 * The FBI's X-Files Division.
 * The NSA is becoming more and more referenced in fiction, such as Seven Days, Jake 2.0, and Star Trek. Until comparatively recently, of course, the government's official stand was that the NSA was itself fictional. Government employees that knew otherwise actually hung a lampshade on it, dubbing it No Such Agency.
 * The NSA is also often shown carrying out activities well outside its real-world mission of communications and cryptography intelligence and counter-intelligence. In the real world, for example, it does not employ James-Bond-style covert agents or snipers, and plays no role in domestic law enforcement.
 * That's what they want you to think!
 * The Organization for Scientific Investigation and Research (OSIR) featured in Psi Factor is allegedly a genuine international non-governmental organization, though the TV show (presumably) veered off the actual organization by a pretty wide margin.
 * Monty Python's Flying Circus: The British Dental Association is a bit of a subversion. While the show portrays it as one of these, they're quite mundane in real life.
 * Fringe has the eponymous FBI "Fringe Division", which works out of a basement at Harvard and consists of an Action Girl, a Mad Scientist, his Deadpan Snarker son, The Chick and the Team Pet reporting to the Bald Black Leader Guy.
 * In an alternate universe Fringe Division is the main investigative arm of the Department of Defense and reports directly to the Secretary of Defense. The FBI no longer exists and Homeland Security was never created (since 9/11 wasn't as disastrous) in that version of the United States.
 * Cold Squad and Waking the Dead introduced fictional police Cold Case divisions before such things began to pop up timidly in Real Life. Cold Case itself avoids the trope portraying the characters as regular Homicide detectives, but in season 7, just as the willing suspension of disbelief was being too stretched (and the perspective of cancellation seemed sure) the writers had the two main characters be offered a position in a projected Cold Case FBI Unit.
 * Walker, Texas Ranger, which depicts the Ranger Division (state investigation bureau) of the Texas Department of Public Safety.
 * Meyers in Murdoch Mysteries is a secret agent working for the Canadian Department of Militia and Defence (about twenty years before it existed in Real Life).
 * Criminal Minds features stars the members of the BAU (an actual division of the FBI). The CIA and Interpol also appear in a few episodes.

Video Games

 * The NSA is becoming more and more referenced in fiction such as Splinter Cell, Perfect Dark, etc. Until comparatively recently, of course, the government's official stand was that the NSA was itself fictional. Government employees that knew otherwise actually hung a lampshade on it, dubbing it No Such Agency.
 * The NSA is also often shown carrying out activities well outside its real-world mission of communications and cryptography intelligence and counter-intelligence. In the real world, for example, it does not employ James-Bond-style covert agents or snipers, and plays no role in domestic law enforcement.
 * In Deus Ex, FEMA is the agency in charge of distributing the Ambrosia vaccine . Walton Simons is the head of FEMA.
 * Death To Spies is named after the Soviet counterintelligence agency SMERSH (whose name is an acronym meaning just that); the player takes the role of a counterintelligence agent and spy working for them during WWII.
 * Gex's father used to work for NASA when he died in an incident involving eating tapioca pudding in zero gravity. After the family later became rich, Gex's mother bought 51% ownership of it, fired everybody, and turned Mission Control into a Suck E. Cheese's.
 * The CIA, KGB, GRU, DARPA, US Department of Defense, and several other real-world agencies play prominent roles in the Metal Gear series.
 * Nelson Tethers: Puzzle Agent: Nelson works for the FBI, Puzzle Division. In fact, he's the division's only agent. A friend of his works for their Vegetable Division. Not that the game takes itself very seriously.
 * Street Fighter: Chun-Li is an INTERPOL agent.

Western Animation

 * The DMV (Department of Motor Vehicles), employers of Patty and Selma. Also seen in Family Guy.
 * The main character on American Dad works at the CIA.
 * In a rarer non-spying example, The Secret of NIMH, with the National Institute of Mental Health. (Who probably weren't very happy about the depiction...let alone the sequel)
 * INTERPOL, Inspector Gadget.
 * The DMV in Megas XLR, which can impressively impound and later boot an 80-foot tall war mecha.