Two explosions rocked the vessel early Wednesday, trapping 18 sailors and sending three others jumping to safety over the side.
The submarine was in the naval dockyard, a high-security area in Mumbai.
Rescuers initially thought the trapped sailors may be alive in an air pocket, but the conditions of the four bodies removed Friday diminished that hope, Press Trust of India reported.
"The damage and the destruction within the submarine around the control room area indicate that the feasibility of locating bodies of the personnel in the forward part of the submarine is also very remote as the explosion and very high temperatures, which melted steel within, would have incinerated the bodies too," a release from the navy said.
The navy said accessing the interior of the submarine was a slow-going process and they were unable to attempt to do so until hours after the explosions because the water was boiling hot.
"Access to the inner compartments of the submarine was almost impossible due to jammed doors, distorted ladders, oily and muddy water inside the submerged submarine, resulting in total darkness and nil visibility even with high-powered underwater lamps," the release from the navy said.
Mohan Guruswamy, a military analyst with the Observer Research Foundation, said he visited the submarine the day before the accident and found it to be "in great shape."
He speculated the cause of the explosions may have been the mishandling of munitions by personnel, The New York Times reported.
"The feeling among naval officers is that while loading the missiles, something happened," he said.
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