The case over the incident yesterday was registered at the Yellow Gate police station in south Mumbai under Section 174 of the Code of Criminal Procedure, said Additional Commissioner of Police, Krishna Prakash.
The bodies of the two naval officers have been taken to the government-run JJ hospital here for post-mortem and will be handed over to their family members later tonight, police said.
Earlier today, Indian Navy confirmed the deaths of the two officers who had been reported missing in the mishap.
The bodies of Lieutenant Commander Kapish Munwal (28) of Delhi and Lieutenant Manoranjan Kumar (26) of Jharkhand were found in a compartment in the vessel after it returned to the harbour.
The Russian-made INS Sindhuratha was on a routine training and work-up (inspection) off Mumbai coast early yesterday when smoke was reported in the sailors' quarters of compartment number three, Navy said.
The smoke soon engulfed the submarine and seven affected sailors had to be airlifted to a hospital in Mumbai even as Munwal and Kumar were initially reported as missing.