| S.No | Name | Assumed office | Left office | Notes |
| 1 | Captain P. S. Mahindroo | 16 February 1961 | 16 April 1963 | Commissioning CO. Later Chief of Materiel. |
| 2 | Captain Nilakanta Krishnan DSC | 17 April 1963 | 16 November 1964 | Flag Officer Commanding-in-Chief Eastern Naval Command during the Indo-Pakistani War of 1971. |
| 3 | Captain V. A. Kamath | 16 November 1964 | 4 November 1966 | Flag Officer Commanding Southern Naval Area during the Indo-Pakistani War of 1971. Founding Director General of Indian Coast Guard. |
| 4 | Captain Jal Cursetji | 4 November 1966 | 8 December 1967 | Later Chief of the Naval Staff. |
| 5 | Captain E. C. Kuruvila | 8 December 1967 | 5 December 1969 | Flag Officer Commanding Western Fleet during the Indo-Pakistani War of 1971. Later Flag Officer Commanding Southern Naval Area. |
| 6 | Captain Kirpal Singh | 5 December 1969 | 15 January 1971 | Later Flag Officer Commanding Western Fleet. |
| 7 | Captain S. L. Sethi NM | 15 January 1971 | 30 June 1971 | Later Vice Chief of the Naval Staff. |
| 8 | Captain Swaraj Parkash MVC, AVSM | 1 July 1971 | 24 January 1973 | Later Vice Chief of the Naval Staff and Director General of Indian Coast Guard. |
| 9 | Captain M. K. Roy AVSM | 3 January 1974 | 8 February 1976 | Later Flag Officer Commanding-in-Chief Eastern Naval Command. |
| 10 | Captain R. H. Tahiliani AVSM | 8 February 1976 | 26 December 1977 | Later Chief of the Naval Staff. |
| 11 | Captain J. C. Puri VrC, VSM | 26 December 1977 | 5 March 1979 | |
| 12 | Captain R. D. Dhir | 5 March 1979 | 15 June 1979 | |
| 13 | Captain S. Bose | 15 June 1979 | 2 April 1981 | |
| 14 | Captain Arindam Ghosh VSM | 2 April 1981 | 27 August 1982 | Later Fortress Commander, Andaman and Nicobar Islands. |
| 15 | Captain KASZ Raju NM | 27 August 1982 | 19 November 1984 | Later Flag Officer Commanding-in-Chief Western Naval Command. |
| 16 | Captain S. K. Gupta MVC, NM | 19 November 1984 | 17 March 1986 | |
| 17 | Captain P. A. Debrass AVSM, NM | 17 March 1986 | 8 August 1988 | Later Flag Officer Commanding Maharashtra Naval Area. |
| 18 | Captain B. S. Karpe | 11 October 1988 | 22 October 1989 | |
| 19 | Captain R. N. Ganesh AVSM, NM | 22 October 1989 | 3 January 1991 | Later Fortress Commander, Andaman and Nicobar Islands and Flag Officer Commanding-in-Chief Southern Naval Command. |
| 20 | Captain Raman Puri VSM | 3 January 1991 | 25 June 1992 | Later Chief of Integrated Defence Staff. |
| 21 | Captain R. C. Kochchar VSM | 25 June 1992 | 7 September 1994 | Later Flag Officer Commanding Maharashtra Naval Area. |
| 22 | Captain K. Mohanan | 7 September 1994 | 7 August 1995 | |
| 23 | Commander H. S. Rawat | 20 July 1996 | 31 January 1997 | Last Commanding Officer. |