The Navy chief today said that prima facie didnot point toward sabotage but currently they were not ruling out the possibility completely.
The Navy has also set up a inquiry panel which would give its report in four weeks.
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There were 18 persons on board the 2,300 tonne submarine, powered by a combination of diesel generators and electric batteries, a defence spokesperson said.
Defence Minister A K Antony confirmed the death on board the Kilo class warship INS Sindhurakshak but gave no details on the casualties.
Earlier he briefed Prime Minister Manmohan Singh about the mishap. Navy Chief Admiral D K Joshi has also reached Mumbai.
Naval sources said the blast took place in the front portion of the 16-year-old submarine which housed the torpedoes.
The navy has ordered a board of inquiry to probe the explosion and subsequent fire in the submarine, he said.
Fire tenders from the naval dockyard as well as the Mumbai Fire Brigade were immediately pressed into action, he said.
However, due to the explosion, the submarine has submerged at the dock with only a portion visible above the surface, a defence statement said.
The statement said efforts are on to ascertain the safety of the personnel and salvage the submarine.
The submarine had returned after a major upgrade programme in Russia 3-4 months ago and was capable of carrying a potent weapons package including the anti-ship 'Club' missiles.
INS Sindhurakshak was not on active duty at the time of the accident, Navy sources said.
The incident has come at a time when the Navy is faced with a depleting submarine fleet.
Commodore (retd) Uday Bhaskar, a former IDSA director, said since the rate of induction of new platforms has not kept up with the kind of wear and tear that a submarine would undertake, the net result is that the Navy's submarine fleet is depleting and the operation load is increasing.
"The fact that the Sindhurakshak (incident) has happened, it is going to have its own adverse impact," he said.
Vice Admiral (retd) A K Singh said an internal explosion in a submarine could be caused by either material failure or by not following standard operating procedure.
He said he suspected that hydrogen gas generated during charging of the batteries of the submarine could have led to the fire which could have spread to the missile compartment area of the warship, causing the massive explosion.
In 2010, a fire broke out on board Sindhurakshak leaving a sailor dead and two others injured. That mishap was caused by an explosion in its battery compartment.
India had bought the submarine from Russia as part of a deal in the early 1980s and the warship was commissioned in 1997. It was the ninth of the 10 'Sindhugosh' class diesel- electric vessels that the Navy has in its 16-strong submarine fleet.
Former navy chief Admiral (retd) Sushil Kumar said Sindhurakshak was a frontline submarine and had been recently modified.
"It was operational and the mishap is indeed a setback," he said.
Kumar said this is not the first time that such an incident has taken place. "There is a professional determination to set things right and everything will be back in order," he said.
In the last few years, there have been several mishaps involving naval vessels. In 2008, another vessel of the Kilo class, INS Sindhugosh, collided with a merchant vessel off Mumbai while participating in a naval exercise.
In 2011, a surface warship INS Vindhyagiri caught fire when it collided with a merchant vessel near the Mumbai harbour while returning from a picnic with families of group of officers deployed on board.
On its way back, it hit another ship leaving the harbour. Nobody was injured but the warship was virtually ruined.
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