(covers information from several alternate timelines)
A security protocol was a command authorization code-protected computer program regarding the security aboard a starship or space station.
In 2258, James T. Kirk recorded a log in which he accused then-acting captain Spock of marooning him on the planet Delta Vega, an action he believed to be a violation of Security Protocol 49.09, which regarded treatment of prisoners held on a starship. (Star Trek)
Commander William T. Riker enabled the security protocol aboard the USS Enterprise-D by using "Riker Omega Three". (TNG: "Power Play")
When a Starfleet officer was captured by an enemy, his access codes and security protocols were changed automatically. (TNG: "Chain Of Command, Part II") In addition, security protocols were changed when the same crime was performed in the same area aboard a space station. (DS9: "Looking for par'Mach in All the Wrong Places ")
Aboard Deep Space 9, Commander Benjamin Sisko and Odo were the only persons who could activate a level five security protocol. (DS9: "Dramatis Personae") Odo himself designed the security protocols aboard Deep Space 9 to generate some "nasty feedbacks" when accessed. (DS9: "A Simple Investigation")
When Jadzia Dax and Miles O'Brien boarded a subspace relay station in the Callinon system, Dax noted it was too fast possible and asked if they activated any kind of security protocol. (DS9: "The Search, Part I")
Elim Garak was able to rewrite Cardassian security protocols. (DS9: "Civil Defense")
In an alternate timeline, Admiral Strickler questioned and accused Harry Kim of breaking into classified files and forging Voyager security protocols. (VOY: "Non Sequitur")
In 2373, the transporter security system on Deep Space 9 failed to detect a remat detonator hidden somewhere on Trentin Fala's person, despite being programmed to do so. This lead Jadzia Dax to speculate that whoever planted the device on understood the space station's security protocols well. (DS9: "The Darkness and the Light")
The same year, someone bypassed the security protocols aboard the USS Defiant and changed the flight plan. (DS9: "Children of Time")
After Tuvok neglected to allow Neelix on his security rounds, Neelix assured him that he had completed his study of starship security protocols and that he felt Tuvok should find that he was "fully qualified to serve in the capacity of a Starfleet security officer. Junior grade, of course." (VOY: "Fair Trade")
In 2375, during the waning days of the Dominion War, members of Rusot's terrorist cell acquired a Cardassian shuttle, with up-to-date security protocols, for use to transport Rusot, Damar, Elim Garak, Kira Nerys, and Odo to infiltrate the repair facility in the Kelvas system. (DS9: "Tacking Into the Wind")
In 2377, the Dralian salesman Gar evaded all of the USS Voyager's security protocols. (VOY: "Critical Care")