The Russian-registered vessel sent out Mayday signals on Sunday morning sparking a huge search and rescue operation in stormy weather conditions.
Amurskaya pictured after she ran aground on 4 June 2012. Picture: Igor Savitskiy
By darkness on Sunday, no trace of the freighter - named Amurskaya - was found.
An amphibious Be-200 plane was deployed from Khabarovsk by the Russian Ministry of Emergency Situations, but it returned to base on Sunday night.
A tanker - Novik - was in the vicinity and it continued the search overnight for survivors.
Following the Mayday signal, radio contact with the Amurskaya was lost.
Heavy rain, strong winds, low clouds and waves swelling to some four metres were reported by Itar-Tass news agency.
The cargo vessel was sailing from Neran on the Uda River in Tuguro-Chumikansky district of Khabarovsk region. It was bound for the port of Okhotsk, and was carrying ore, it was reported.
Earlier there were claims there maybe an innocent explanation to the emergency signal received from the Amurskaya.
'The Amurskoye motor ship disappeared three hours ago after sending a distress signal. We are currently searching for the ship but have so far failed to find it,' the Yuzhno-Sakhalinsk Sea Rescue Coordination Centre told RIA Novosti news agency.
'An emergency beacon was activated. Probably, it simply fell over the board. That is why, we can't yet say that the ship has sunk.'
The 55-metre long vessel was near the Shantar islands in the southwest of the Sea of Okhotsk when it sent the signal. All 11 crew are from the Far East of Russia, it was reported.
However, Mikhail Voitenko, the editor of the respected Maritime Bulletin - http://www.odin.tc - suggested there was a confusion over the name of the 'stricken' ship with some reports naming it as the Amurskoye, a fishing not a cargo vessel.
He also claimed, contrary to latest news agency reports, that 'there are 11 passengers on board and unknown number of crew'.
It is the second incident in a few months for the Amurskaya. In June she ran aground in Okhotsk port with 500 tons of food badly needed by locals.
The Amurskaya was the first freighter to arrive to Okhotsk following the ice-melt.
Six days later the cargo ship was floated after her cargo was partially offloaded.
Archeologists discovered a new stone bracelet, two sharp pins, a marble ring and fox tooth pendants.