A security subroutine was a subroutine in computer programs related to various security-related matters.
In 2371, Tuvok altered the security subroutines of USS Voyager's transporter, so Joseph Carey's security codes were no longer accepted to initiate beaming. (VOY: "Prime Factors")
In 2372, Tuvix worked on a proximity detector problem in the security subroutine and solved in a few hours, while Tuvok had predicted it would take up to ten days. (VOY: "Tuvix")
While trapped aboard the Nyrian biosphere vessel in 2373, Tuvok suggested to disable the entire security subroutine to gain access to the vessel's systems. (VOY: "Displaced")