In the episode of DS-9 "Inquisition" Slone mentions to Bashir that Section 31 has been part of the Federation since it's original charter. Does anyone recall any mention of Section 31 in any other Trek Series or Films.
It does make sence that the Federation would have it's own Internal Intelligence Branch. The Romulans have the Tal-Shair, and the Cardassians have the Obsidian Order. It would seem to me that it would be a bit nieve for the Federation to not have internal security of it own.