Based on the guidance of "the Armed Forces to reorganize Headquarters" of the Ministry of National Defense, MND, the original logistics command is deactivated on January 1, 2006. Moreover, according to an official policy that aims to trim and streamline high secretary and fill basic level, the navy organization is adjusted. General speaking, the businesses of the original Navy Logistic Command, which include the management of purchasing, supplies, logistics information and management of repairable tools are all transferred to the Combined Logistics Command , MND and Procurement Center , MND. The obligation of ship policy, Combat System, Supplies, Aviation and Integrated Logistics, Base Service are transferred to Logistics Office, MND and the correlated organization in Navy. Four Navy Support Logistics Commands and the Naval Combat Systems Facility were directly supervised by the Navy Command.
Naval Maintenance & Repair Command is directly subordinated to the Navy Headquarters, MND and executes jurisdiction over the Logistic and Supprt Commands in Tsoying, Suao, Keelung, and Makung and the Naval Combat Systems Facility as well as the Naval Supply Head Depot.