The secondary command processors were computer components aboard a Federation starship that were necessary to carry out the self-destruct sequence. These processors were located on deck 12 of an Intrepid-class starship, on the starboard ventral.
In 2372, Seska arranged for a series of seemingly random Kazon raider attacks on the USS Voyager, doing minor damage each time to the secondary command processors. The repeated attacks complicated repair efforts, ultimately resulting in the complete destruction of the processors, which Ensign Harry Kim estimated would take at least two days to rebuild from scratch, assuming Voyager wasn't attacked again. She was thus ultimately able to prevent Captain Kathryn Janeway from initiating the auto-destruct when the Kazon-Nistrim overwhelmed Voyager's defenses, though nobody onboard was able to guess her goal beforehand, as the secondary command processors were considered a "nonessential area." (VOY: "Basics, Part I")