Starfleet Security Starfleet Security was an agency in Starfleet . This agency was one of the oldest with its origins dating back to the United Earth Starfleet . The agency was located at Fleet Operations Center in San Francisco , Earth , Sol Sector . The agency was responsible for safeguarding the Federation from internal and external threats , for conducting criminal investigations , and for guarding Federation facilities . ( , directories ) 22nd century . was a member of Starfleet Security until 2149 , at which point he became a member of the covert operations group known as Section 31 . ( ) In 2154 , Commander was an officer in Starfleet Security . When Doctor Phlox was abducted in San Francisco as part of a Klingon plot , she was in charge of the investigation . ( ) That same year , the dedication plaque of the listed the names of notable officers assigned to this agency who protected the shipyard where the starship was constructed and tested . ( , Columbia dedication plaque ) In January of 2155 , the directory placards at Starfleet Command ' s Fleet Operations Center , Sol Sector listed the names of notable officers who had offices at the center . ( , directories ) 24th century . 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 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 . ( ; ) In 2367 , Vice Admiral Thomas Henry , who was attached to Starfleet Security , boarded the to observe a hearing overseen by former Starfleet admiral Norah Satie , concerning an attempt to uncover a supposed conspiracy at the heart of Starfleet . ( ) 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 . ( ) Starfleet Security often sent Odo criminal activity report s . ( ) Starfleet Security had documented several incidents of Cardassian s being surgically altered with the purpose of infilitrating an enemy . It was determined by the crew that Seska was another of these incidents – surgically altered as a Bajoran , she infilitrated the Maquis . ( ) A Starfleet Security investigation determined that Ambassador Krajensky had been kidnapped or killed by the Dominion on his way to Risa . ( ) " In an alternate timeline experienced by Kim in 2372 , Admiral had a meeting with the female head of this branch at eleven hundred hours . " ( ) 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 . ( ) After Sisko was attacked by a member of the Cult of the Pah - wraiths in early 2375 , he gave a statement to Starfleet Security . ( ) Backgound information . According to the , the prison guards from were wearing the Starfleet insignia for Starfleet Security on their left breast .