Serdyukov said the crew was rescued without a shot being fired.
He said the Arctic Sea merchant ship was hijacked in Swedish territorial waters in the Baltic Sea.
The Arctic Sea vanished while sailing from Finland to the Algerian port of Bejaia, where it was due to have docked on August 4 with a $1.3m load of timber.
Earlier, relatives of the crew appealed to Vladimir Putin, Russia's prime minister, for a criminal investigation into the affair.
The Kremlin ordered Russian warships to join the hunt for the 4,000-tonne, 98-metre bulk carrier after it went missing in the English Channel.