The freighter "Amurskaya" had been missing since October 28, when it sent a distress call from the Sea of Okhotsk.
The ship was found by divers in about 75 meters of water on November 7.
The Transportation Ministry in a statement said its 11 crew members remain unaccounted for.
Police have lodged criminal charges against the ship's owner, who is also the director of the Nikolayevsk-on-Amur port where the ship is registered.
He has been charged with safety rules violations.
The ship was reportedly carrying some 100 tons of gold ore more than its maximum capacity.
No details on how much gold the ore could contain have been released.