In the 2350s, a secret group at Starfleet Security engaged in an illegal operation to develop a Starfleet phasing cloaking device, in direct violation of the Treaty of Algeron. The phasing cloak was tested aboard the USS Pegasus in 2358, under the command of Captain Erik Pressman, but ended in disaster when it appeared the Pegasus was destroyed. The entire affair was subsequently covered up by Starfleet Intelligence. Twelve years later, the Chief of Starfleet Security at the time, Admiral Raner, oversaw an operation to retrieve the experimental cloaking device. (ENT: "These Are the Voyages..."; TNG: "The Pegasus")
In 2367, Vice Admiral Thomas Henry, who was attached to Starfleet Security, boarded the USS Enterprise NCC-1701-D to observe a hearing overseen by former Starfleet admiral Norah Satie, concerning an attempt to uncover a supposed conspiracy at the heart of Starfleet. (TNG: "The Drumhead")
In 2371, due to skepticism related to Constable Odo's abilities as security chief, Starfleet Security assigned Lieutenant Commander Michael Eddington to Deep Space 9, to oversee security issues pertaining to Starfleet matters. (DS9: "The Search, Part I")
In 2372, Admiral Leyton made Benjamin Sisko acting head of Starfleet Security, in face of the apparent Changeling infiltration of Starfleet. In this capacity, Sisko discovered that Leyton was using the recent bombing of the Antwerp Conference as an excuse to attempt to seize power by the military, by instilling paranoia about the threat posed by the Dominion. Sisko subsequently uncovered Leyton's conspiracy, forcing him to resign, and returned to Deep Space Nine. (DS9: "Homefront", "Paradise Lost")
- Malcolm Reed was posted as armory officer - prior to the Federation Starfleet Security being established - aboard the Enterprise.
- One of Hikaru Sulu's assignments aboard the USS Enterprise from 2265 through 2270 was that of Security officer.
- Pavel Chekov was in charge of security on the USS Enterprise-A in 2273.
- Tasha Yar served as security officer aboard the USS Enterprise-D.
- Worf served as security officer aboard the USS Enterprise-D after Yar's death.
- Odo performed station security on Deep Space 9, although he was not part of Starfleet Security.
- Michael Eddington was responsible for Starfleet security on Deep Space 9 and the USS Defiant in 2371 and 2372.
- Aboard the USS Voyager, Tuvok was the security officer.