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The accident, which happened while the submarine was on sea trials in the Pacific Ocean, was the deadliest to hit Russia's navy since the Kursk nuclear submarine exploded beneath the Barents Sea in 2000, killing all 118 sailors on board.
Prosecutors investigating the latest incident said they suspected the victims died after inhaling a toxic gas used as a fire suppressant when the vessel's fire extinguishing systems went off unexpectedly. It was not clear why the portable breathing gear usually issued to Russian submarine crews did not save them.
"20 people died," the Prosecutor-General's Office said in a statement. "Results of a preliminary investigation show that death occurred as a result of freon gas entering the lungs."
A navy spokesman said the submarine's reactor was not damaged and was the vessel now moored at the Bolshoi Kamen naval base on the Pacific. "It returned under its own steam, under escort by the Sayany rescue vessel. It is being moored at the anchorage," spokesman Captain Igor Dygalo said. "The radiation levels on the ship are normal."
Another 20 people were injured and transferred to a military hospital in Vladivostok.
President Dmitry Medvedev ordered the Defense Ministry to carry out a full inquiry, the Kremlin press service said.
The Kremlin is seeking to establish itself as a global power and is using the military to project its influence. A flotilla of ships is heading to U.S. foe Venezuela for the first such maneuvers in the Caribbean Sea since the Cold War ended.
But analysts say the navy in particular is still struggling with the legacy of over a decade of under-funding, despite a cash injection in the past few years.
"This most recent incident signals that, though Russia is increasingly assertive and aggressive on the geopolitical stage, it still faces very real challenges in terms of the revitalization of its naval power," Stratfor, a U.S.-based consultancy, said in a commentary.
The navy said 208 people - or nearly three times more than its usual crew - were on board the submarine when the fire extinguishing system went off. Many of them were specialists from the vessel's manufacturer who were preparing to hand it over to the navy.
Seventeen of the dead were employees of Amur Ship-Building Enterprise and three were sailors, prosecutors said.
The vessel was underwater when the gas was released; RIA news agency quoted a naval source as saying.
"One can assume that the submariners did not notice the release of the gas, and when they did feel it, it was too late," the source told the agency.
One military analyst said it was possible not all of those on board had breathing gear.
"It is possible that some of the people lingered (putting on the apparatus) or they did not have the apparatus at all," Ruslan Pukhov, director of the Center for Analysis of Strategies and Technology, told the Ekho Moskvy radio station.
The navy did not identify the submarine. Russian news agencies quoted naval sources as saying it was the Nerpa, classified by NATO as an Akula-class attack submarine. Media reports said Russia had planned to lease the submarine to the Indian navy, but there was no confirmation of this.