Rescuers have had no contact with any of the crew since the blasts at the Mumbai navy base. Navy divers had opened one of its hatches but had not yet been able to enter the submarine because it was dark and full of muddy water.
Admiral D.K. Joshi, the navy chief, said: “We hope for the best but we have to prepare for the worst.”
The Russian-built conventionally-powered submarine had been damaged in another deadly blast in 2010 and was brought back into service only a few months ago.
The explosions in its torpedo compartment sent a huge fireball into the air and sent nearby sailors jumping into the sea in panic.
Because the submarine was docked, a small watch crew was on board when the blasts occurred.
The 16-year-old submarine, INS Sindhurakshak, also suffered an explosion in 2010 that killed one sailor and injured two others. The navy said that accident was caused by a faulty battery valve that leaked hydrogen.
The sub recently returned from Russia after a two-year refit, overhaul and upgrade. Russian ship repair company Zvyozdochka said the blasts were unrelated to its repair work.
“According to the members of our warrantee group, the vessel was functioning properly and had no technical faults at the time of the incident,” a spokesman said.
India is facing a shortage of submarines because of obsolescence. The government has authorised the navy to have up to 24 conventional submarines, but it has just 14.
Last year India acquired a Russian Nerpa nuclear submarine on a 10-year lease at a cost of nearly £1bn.
India has also designed and built its own nuclear submarine. The navy activated the atomic reactor on that vessel on Saturday and could deploy it in the next two years.