In 1961, Kamath moved to Naval HQ having been appointed Director of Naval Plans for the second time, this time in the rank of captain. He served in this appointment during the Annexation of Goa. In late 1964, Kamath was appointed the third commanding officer of the Navy's flagship - the aircraft carrier . He took command from Captain Nilakanta Krishnan in November. In early 1965, he led the ship in large air-sea exercises in the Arabian Sea. The Chief of the Naval Staff Vice Admiral Bhaskar Sadashiv Soman flew his flag on the flagship "Vikrant". During the Indo-Pakistani War of 1965, the "Vikrant" was under refit and did not sail and participate. However, her squadrons - INAS 300 and participated in the war. In late-1966, Kamath was selected to attend the Imperial Defence College.