Speaking Wednesday at the navy's Arctic base of Severomorsk, he praised the vessel's crew for "heroic" action, saying they sacrificed their lives to rescue a civilian expert and save the ship after the fire erupted.
The Kremlin said details of the accident would not be made public but denied claims that an explosion took place on board the submarine.
They inhaled toxic smoke produced by the fire, the Kremlin said.
The Russian navy also uses Priz-class and Bester-class deep water vehicles, which have a hull built of titanium and are capable of operating at a depth of 1,000 meters.
Russian Federation is in an global race to stake territorial claims in the Arctic, because the pristine region is believed to be rich in oil and gas and other minerals.
According to the official, the sailors of the submarine has poisoned with burning products.
The submarine is made up of a series of interconnected spheres that allow it to resist water pressure at great depths.
Russian President Vladimir Putin said that the submarine was on a special mission, and that among the 14 dead, 7 were first rank captains and 2 were Heroes of Russia, the highest military honour.More news: Warriors Hold On To Kevon Looney; Jordan Bell Signs With Minnesota
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The official investigation reported that the last survivors only resisted four hours after the explosion.
On July 1, a fire broke out on a naval deep-sea research vessel, while the crew was taking biometric measurements.
"The submariners acted heroically in the critical situation", he said.
In his conversation with Shoigu on Tuesday, Putin only described the affected submersible as "an unusual vessel" tasked with "research" and manned by "a highly professional crew". "I offer my honest condolences to the families of the victims". Putin is set to visit the Vatican Thursday for a meeting with the pope.
In 2008, 20 people died in a gas leak on the submarine K-152 Nerpa in the Sea of Japan.
Moscow says it is fully compliant with the INF treaty negotiated by U.S. President Ronald Reagan and Soviet leader Mikhail Gorbachev, which eliminated the medium-range missile arsenals of the world's two biggest nuclear powers. Some Russian officials have claimed that the sub can travel as deep as 19,685 feet, although this has yet to be independently verified.
United States authorities have previously accused Russian Federation of attempting to intercept or sabotage communications via the Losharik's extraordinary deep sea capabilities to tamper with or even sever underwater cables.
THE latest Russian submarine tragedy is causing some commentators in the West to point out that Moscow's renewed and reequipped armed forces are still subject to the procedural shortcomings that saw the humiliating 2000 loss of the nuclear sub Kursk in which the entire 118 crew perished.
He also confirmed the Putin was informed immediately of the disaster at sea.