The Command is organised as shown on the Flow Chart placed at Appendix. Under the C-in-C, there are both Staff and Operational authorities. The Staff Channel is headed by the Chief of Staff, who has under him the Chief Staff Officers, who head respective functional divisions. The various Operational authorities under the C-in-C include the following:-
- The Flag Officer Commanding Western Fleet. FOCWF commands all the major surface combatants allocated to the Western Fleet.
- The Flag Officer Commanding, Maharashtra and Gujarat Naval Area. FOMAG is responsible for the coastal defence of all ports and coastal areas in Maharashtra and Gujarat.
- The Flag Officer Commanding, Goa Naval Area. The Fixed Wing Shore based Naval Air assets of this Command are under the Flag Officer Commanding, Goa Naval Area.
- The Flag Officer Defence Advisory Group. FODAG is the advisor to the Govt of India on all matters regarding security of our offshore installations.
- The Flag Officer Commanding Karnataka Naval Area. FOK, with his headquarters at Karwar, is responsible for the coastal defence of all ports and coastal areas in Karnataka.
- The Commodore Commanding Submarines. The submarines of the Command are placed under the Commodore Commanding Submarines.
- The Commodore Commanding, 22 Missile Vessel Squadron. The Commodore Commanding, 22 Missile Vessel Squadron, also referred as Captain (K) or K22, is under the operational command of Flag Officer Commanding, Maharashtra and Gujarat Naval Area.