The hijackers had approached the Arctic Sea in a dinghy, claiming they needed help to repair their vessel, Russia's Interfax news agency quoted Mr Serdyukov as saying.
But once on board the cargo ship, they threatened the crew with guns and forced them to sail south, the defence minister said.
Second attack?
The suspects include four Estonians, two Latvians and two Russians.
Mr Serdyukov said an investigation was under way aboard the Russian warship Ladny, where the Arctic Sea's 15-strong crew members and the suspected pirates were being questioned.
The Ladny joined the hunt for the missing ship last week after Moscow deployed the strength of its Atlantic fleet to find the Maltese-flagged ship.
Malta's Maritime Security Committee says it continued to track the ship after it was reported missing.
"There was consensus amongst the investigating authorities of Finland, Malta and Sweden not to disclose any sensitive information, in order not to jeopardise the life and safety of the persons on board and the integrity of the ship," the committee said in a statement on Tuesday.
Carrying timber reportedly worth $1.8m (£1.1m), the 4,000-tonne Arctic Sea sailed from Finland and had been scheduled to dock in the Algerian port of Bejaia on 4 August.
The crew reported having been boarded by up to 10 armed men as the ship sailed through the Baltic Sea, but the intruders were reported to have left the vessel on an inflatable boat after 12 hours.
Ransom demand
There are also reports of the ship having been attacked a second time off the Portuguese coast.
However, the vessel's operators said they had no knowledge of the incident and Portugal said the ship was never in its territorial waters.
Before being found, the last known contact with the crew was when the Arctic Sea reported to British maritime authorities in Dover as it passed through the busy shipping waters of the English Channel.
It was then sighted in the Bay of Biscay on 30 July.
Last weekend, a multinational investigation was launched after police in Finland said a ransom demand had been made, while emphasising that they could not confirm its authenticity.
The Arctic Sea was eventually found on Sunday night 300 miles (480 km) off Cape Verde in the Atlantic Ocean.
The Maltese authorities say they are now trying to ensure that the Arctic Sea is granted a safe berth "to allow for the required investigations into the seaworthiness of the ship".
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