The crew was poisoned by fumes as the vessel was taking measurements in Russian territorial waters on Monday.
The ministry gave no details about the type of vessel. But Russian media reports say it was a nuclear mini-submarine used for special operations.
The fire was later put out and the vessel is now at Severomorsk, the main base of the Russian Northern Fleet.
The defence ministry did not say how many crew members were aboard at the time. Reports in local media say several crew were injured and taken to hospital.
An investigation into the incident has begun under the commander-in-chief of the navy.
Russian President Vladimir Putin later on Tuesday pulled out of a scheduled event in the Tver region, north-west of Moscow, to discuss the issue with Defence Minister Sergei Shoigu.
Mr Putin described the incident as a big loss for the Russian Navy, and expressed "sincere condolences" to the victims' families.
Seven captains and two service personnel awarded Russia's highest honorary title, Hero of the Russian Federation, were among those who died on board the vessel, the president said.
Mr Shoigu was ordered to go immediately to Severomorsk.
It's still not clear what caused the fire, which the crew ultimately brought under control; we don't know how many men survived.
And there are still questions over exactly what vessel was involved.
President Putin said the dead included two heroes of Russia and seven captains "of the first rank"- which seems unusually senior - for research work.
Some media in Russia are citing sources saying they could have been on board a nuclear-powered submarine, possibly even the secretive AS-12. It is thought to be used for highly sensitive missions.
Mr Putin returned especially to the Kremlin from out of town to order his defence minister to oversee the investigation.
The president is clearly keen not to repeat his disastrous handling of the Kursk submarine disaster in August 2000, when 118 men died.
That accident was shrouded in secrecy - and Mr Putin initially stayed on holiday for several days.
