The secondary command processors are computer components aboard a Federation starship that are necessary to carry out the self-destruct sequence. These processors are located on deck 12 of an Intrepid-class starship.
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. She was thus ultimately able to prevent Captain Kathryn Janeway from initiating the auto-destruct when the Kazon-Nistrim overwhelmed Voyager's defenses. (VOY: "Basics, Part I")