All 26 Indian crew on board the Indian ship were safe.
Tomy was battling for life on the dismasted sailboat Thoriya with a severe back injury, the officials said.
The Indian Navy said it was in a high state of readiness to "deter, prevent and defeat" any "misadventure" by Pakistan in the maritime domain.
A top navy official said the test-firing yielded desired results.
The Indian Navy said Lieutenant commander D S Chauhan died after 'bravely' leading the firefighting efforts in the affected compartment.
The Navy chief also inaugurated the new Air Traffic Control building there.
On skeletons being seen by the Navy team, the sources said the water inside the mines has high Sulphur content which can decompose the bodies very fast.
Notwithstanding the strain in ties, the navies of India and China carried out a well coordinated operation to rescue a merchant ship in the Gulf of Aden which was hijacked by Somali pirates on Saturday night.
When questioned about the absence of any mention of the Indian Navy's role in the operation, Hua said China's ministry of defence should be approached for details.