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Internal Affairs was a department of Starfleet Intelligence, tasked with investigating possible security threats within Starfleet and ensuring that Starfleet officers acted in accordance with Federation laws.
In 2374, Section 31 operative Luther Sloan posed as a Deputy Director with Internal Affairs, during a covert operation designed to test the loyalties of the genetically-engineered chief medical officer of Deep Space 9, Julian Bashir. Sloan described Starfleet Internal Affairs as a "competent department, but limited". (DS9: "Inquisition")