Granted, it serves an alien government, but in StrikerS, the focus is on the Bureau's homeworld, so it isn't quite so alien anymore.

The Time-Space Administration Bureau of Lyrical Nanoha.

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.The Organization from Haruhi Suzumiya presents itself as possibly being one of these, but later information seems to indicate that it's more of a small group of individuals who happen to be well-connected.The Social Welfare Agency in Gunslinger Girl.It isn't a monolithic entity but is more like an umbrella organization coordinating various semi-independent sections, so a couple of fictional ones would fit the structure just fine. They're intended to be more like fictional branches of the very real (although less than widely publicized) Japanese intelligence establishment. Public Security Section 9 in Ghost in the Shell, as well as the Cabinet Intelligence Agency in Stand Alone Complex 2nd GIG.

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.Dorothea in Fairy Gone, a government office that reports directly to the Prime Minister and is tasked with investigating crimes involving the illegal usage of fairies.Dirty Pair: The Worlds Welfare Work Association (3WA), with troublesome agents Kei and Yuri.Hypnos and DATS in Digimon, MIB agencies.The RAPT (Recently Armed Police Taskforce) in Burst Angel.The titular organization from ACCA: 13-Territory Inspection Dept., an agency that manages the police, fire departments, and various other services in the 13 districts of Dowa Kingdom.

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