The FSI has its Headquarters  at Mumbai and six bases located at Mumbai, Mormugao, Kochi, Chennai, Visakhapatnam and Port Blair.  The Base at Porbandar is not currently operational.  The sanctioned staff strength of the organization is 708.  The Director General heads the organization.  One or two survey vessels are placed at each Base with the required complement of operative staff.  A Zonal Director who is assisted by the scientific, engineering and administrative personnel head each Zonal Base.

In addition the  Marine Engineering Division (MED) [transferred from IFP (NIFPHATT) to the Fishery Survey of India during 2005]  is attached to the  Base of FSI.