It sounds an awful lot like the basic set up for Bureau 13, which was actually a role-playing game.
http://en.wikipedia.org/wiki/Bureau_13
It did have a few novels written for it, none of which I have ever read, so possibly it might be one of those.
Fictionwise has them:
http://www.fictionwise.com/ebooks/a450/Nick-Pollotta/?
(So does Amazon, actually for cheaper)
Not really enough of the blurb to tell if that's what you read or not. Perhaps not, but certain in the same vein