"Radiation in the area of the emergency incident onboard the Tomsk is normal, the reactor had been out of operation since the submarine began undergoing repairs in 2011," a source in the Far East fleet told RIA Novosti.
The fire was put out and all staff evacuated, with no injuries, said the defence ministry statement.
"According to preliminary data, the reason for the fire was violation of welding procedures," it said.
The submarine was being repaired in the Bolshoi Kamen shipyard near the port of Vladivostok.
In late 2011 a massive fire broke out on another nuclear submarine in Murmansk while it was under repairs, injuring nine people. Reports later said that the vessel was armed with long-range missiles.