In June 1961, Krishnan was appointed commanding officer of the Navy's Engineering College INS Shivaji in Lonavala. Shortly thereafter, in December, he was asked by the Chief of the Naval Staff, Vice Admiral Ram Dass Katari, to take command of the "Delhi" immediately and prepare her to put to sea in two weeks. The ship was to participate in the Annexation of Goa providing distant support to the Indian Army units storming Diu. On 11 December, he positioned the ship close to the coast and fired a barrage on the Diu Fortress. She also sunk four ships off the harbour and sent a landing party to the citadel of the fortress and hoist the Indian Flag. After the annexation, he returned to "INS Shivaji" and was in command for a year.