The Nigerian Navy is structured into a Naval Headquarters made up of the Office of the CNS and 8 staff branches each administered by a Branch Chief of flag rank.
These branches are:
- Policy and Plans
- Training and Operations
- Naval Engineering
- Account & Budget
- Naval Safety and Standards
- Office of the Navy Secretary
There are offices that report directly to the CNS, these include Nigerian Navy Transformation Office (NNTO), Project Implementation, Monitoring and Evaluation Directorate (PIMED) and Nigerian Navy Holdings.
There are 5 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) and a Logistics Command (LOG COMD). 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.