None of the crew was injured in the operation, the minister said.
'The investigation into the hijacking is continuing on board the (Russian Navy's) Ladny frigate. We are taking measures to send the crew (of the Arctic Sea) back home,' Serdyukov said.
Russia's Investigation Commission said it launched a criminal probe in connection with the hijacking.
The Maltese-flagged cargo ship, carrying timber, left Finland July 22 en route to Algeria. The ship last made radio contact with British coast guards July 28. Finnish Police confirmed that a $1.5 million ransom demand had been issued.
Last week, President Medvedev instructed the navy to launch a search for the missing ship.