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Federation seems to have plenty of hostile species, both in states of cold and hot war (at different times, Klingons, Romulans, Xindi, Borg, Dominion, etc...)

We know that the concept of intelligence operations exists in Star Trek (for example, Tuvok's mission to infiltrate the Maquis).

But is there canon evidence that there is an actual dedicated "foreign" intelligence branch in the Federation, similar to CIA/NSA; MI6 or GRU/KGB's foreign directorate; dedicated to both human and signal intelligence gathering on non-Federation species? (as opposed to individual Star Fleet officers acting in intelligence capacity).

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Starfleet Intelligence is the main intelligence agency in the Federation. They spied on the Orion Syndicate, Terra Prime, the Klingons, the Romulan High Command, the Maquis, and the Dominion.

Section 31 is more of a rogue agency that was started by and recruited Starfleet officials and officers and that Starfleet took advantage of when their own rules and regulations prohibited action, e.g. the case with the morphogenic virus. Even the name "Section 31" is just a reference to a section of the Starfleet Charter rather than a formal organizational designation.

So Section 31's relationship with the Federation is more like that between Al Qaeda and the former Taliban government of Afghanistan, or that between the Taliban and the Pakistani government (through the ISI).

In fact, Section 31 does not collect intelligence for Starfleet or take orders from the Federation government. They don't provide any actual intelligence to anyone else. All they do is conduct rogue operations which they feel are in the interest of the Federation (or their vision of it), and they do not report to anyone.

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There sort of is: Section 31

Section 31 was the name of an officially-nonexistent and autonomous clandestine organization which claimed to protect the security interests of United Earth and later the United Federation of Planets.

They sort of just spy on everyone, and is everywhere at all times.

It is the group whose building was blown up in Star Trek Into Darkness. They are more significant in DS9.

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Thanks for Star Trek Into Darkness reference. It's not so clear on the movie. –  Magno C Feb 3 at 14:00

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