There are 6 commands headed by Flag Officers Commanding (FOCs) and 5 autonomous units. The commands are made up of 3 operational commands namely: Western, Eastern and Central Naval Commands (WNC, ENC and CNC) which are responsible for the protection and policing of the nation’s maritime environment; a Naval Training Command (NAVTRAC), Logistics Command (LOG COMD) and Naval Doctrine Command (NAVDOC). The autonomous units are the Nigerian Naval Dockyard (NND), Nigerian Naval Shipyard (NNSY), the Naval Ordnance Depot (NOD), Nigerian Navy Holdings Limited (NNHL) and Naval Doctrine and Assessment Centre (NDAC). The NND and NNSY carry out third line maintenance and docking of NN ships while the NOD stores NN arms and ammunition and a limited storage for the NA, NAF and some paramilitary units. These units and facilities enable the NN to maintain the fleet for sustained operations.

Western Naval Command, Apapa, Lagos;

Eastern Naval Command, Calabar;

Central Naval Command;

Naval Training Command, Apapa, Lagos;

Logistic Command, Oghara – Delta State;

Naval Doctrine Command, Victoria Island – Lagos;