The Tass news agency said the operation had been undertaken at 20 minutes past midnight near the port of Murmansk, in the Arctic. It said that the young conscript, who had barricaded himself in the torpedo room, died in the assault.
The man, who was identified as 19-year-old Alexander Kuzminykh, had killed a sentry guarding the vessel early on Friday at the Skalisty base, seized his rifle and went below, where he killed five more men. Two servicemen were then taken hostage and later killed, according to Russian news reports.
A spokesman for the Federal Security Service had earlier said that an anti-terrorist commando unit was ready to act after the conscript's mother, flown to the base from her home in St Petersburg, was unable to persuade him to give himself up.
The Defence Ministry said there were no nuclear weapons aboard the Akula (Shark) class submarine, which is part of the Russian Navy's Northern Fleet, based in and around Murmansk. The submarine's nuclear reactor would not normally be in operation when the vessel was docked.
The assault commandos had attempted to negotiate with Kuzminykh, who was threatening to blow up the vessel. It was unclear if he had access to explosives. The Defence Ministry said there was no danger to the vessel. Though there were no nuclear weapons on board the 110-metre hunter-killer boat, which is capable of sailing underwater for weeks on end, they are sometimes equipped with nuclear-tipped tactical weapons.
Kuzminykh was said to have been in detention on disciplinary charges. Earlier, the Defence Ministry issued a bald statement confirming that there was an "emergency" on a submarine from the Northern Fleet "involving the death of personnel". The incident was sufficiently serious for Admiral Vladimir Kuroyedov, the head of the Navy, to fly to the scene.
The incident served as a further reminder of the deepening despair in the armed forces. It also seems to raise serious questions about security at Murmansk, the base for dozens of Soviet-era nuclear submarines, which rarely sail these days because of the lack of funds for fuel.
Murders and suicides occur with alarmingly regularity in the Russian armed forces, which have long been teetering on the edge of collapse. Lack of wages, hunger and bullyinghave placed servicemen under intense stress.
The worsening economic conditions in Russia, with a devalued rouble, food queues and rising prices, suggest that bloodshed in the armed forces will only get worse.
The list of recent incidents is already alarmingly long: last month a group of soldiers led police on a four-day chase across a remote Arctic peninsula after shooting their way out of jail.
In April a conscript killed three colleagues at a border post in the Far East and in January a private killed seven people on the Pacific island of Sakhalin.
Last November a border guard private massacred five comrades at a post on the Chinese frontier.Reuse content