The NHQ is organized and functions as shown in the organogram below:

To enable the Navy carry out the enumerated roles, it is organised with a Headquarters (BURMA CAMP) where all the policy decisions are made, two operational commands, and a training command. The entire Navy is headed by the Chief of the Naval Staff with established rank of Rear Admiral.

The units and establishments under the Western Naval Command, headquartered in SEKONDI, comprise the Ghana Navy Fleet, the Naval Dockyard Complex, the Ghana Navy Stores Depot, and the Naval Base, Sekondi.

The units under the Eastern Naval Command, with its headquarters in TEMA, include the Naval Base - Tema, the Ghana Navy Band and the Fleet Detachment stationed in the Command.

The units under the Naval Training Command, with its headquarters at NUTEKPOR, include the School of Maritime Operations (SMOPS), School of Marine Engineering and Combat System (SMECS), Supply Application School (SAS), Leadership Training School (LTS), and Naval Base Nutekpor, Sogakope. Currently, the SMECS and LTS are co-located at the WNC and ENC respectively.

Each of the 3 commands is headed by a Flag Officer Commanding (FOC), with established rank of Commodore. The FOC’s are responsible to the Chief of the Naval Staff for the command and control of all the units under command.

The functional departments in the Navy, just like the sister Services, are: OPERATIONS, TRAINING, ADMINISTRATIION, TECHNICAL and SUPPLY.