Russia’s top general hinted yesterday that the ship allegedly hijacked by pirates earlier this month may have been carrying a secret cargo, as it emerged that the country’s Navy tracked the vessel throughout its journey.

President Medvedev sent the Russian Navy to find the Arctic Sea after it apparently disappeared while passing through the English Channel en route to Algeria from Finland. However, the Foreign Ministry in Moscow now says that Russian and international agencies had monitored the ship throughout its strange three-week voyage.

General Nikolai Makarov, the Russian Army’s top general, said that the military would search the vessel thoroughly after it had docked at the Black Sea port of Novorossiysk. “The motives behind the seizure are not wholly clear. We do not know what it is carrying,” he told reporters. “All we know is that it is carrying timber, but an investigation should determine whether it is carrying anything else.”

The Foreign Ministry said that a preliminary search had uncovered no suspicious cargo, but it admitted that there were many “blank spots” in the investigation.

It did insist, however, that the authorities knew where the ship was throughout its mysterious voyage. “Of course, the dry cargo carrier with a displacement of more than 7,000 tonnes was never missing. Its movement was being followed and its co-ordinates were being reported from several sources, including our foreign partners,” the ministry said.

The saga also took a bizarre new twist when the ministry disclosed that the ship’s captain had tried to pass off the Arctic Sea as a North Korean vessel when it was intercepted by the Russian Navy. This is the first time that investigators have implicated the crew in the mystery.

The ministry said that the captain “unexpectedly claimed” to be in charge of a ship called the Chongdin 2 that was carrying timber from Cuba to Sierra Leone. Russian diplomats in Pyongyang checked with North Korean officials and were told that the Chongdin 2 was docked at a port in Angola at the time.

“In view of this information, the command of the Russian Navy decided to examine the ship and the examination confirmed the surmise that it was the Arctic Sea,” the Foreign Ministry said. It gave no indication of how the captain knew of the other vessel’s existence or why the Navy was unable to identify the Arctic Sea from its markings.

The Arctic Sea was listed as carrying timber worth $1.3 million (£800,000), but Alexander Bastrykin, head of the Investigative Committee of the Prosecutor-General’s Office, said: “We do not rule out the possibility that they might have been carrying not only timber. This is why we need to examine the vessel – so that there are no dark spots in this story.”

It even cast doubt on its own initial version of events, that an armed gang had seized the vessel on July 24 and taken the crew hostage. The ministry said that it was “still unclear whether the initial capture of the ship ... and subsequent events are links in the same chain of piracy or not".

The ship and its 15-man crew, all Russian, left Finland on July 22. It was declared missing for more than two weeks after apparently being boarded by an armed gang in Swedish waters. Mr Medvedev sent warships and submarines from the Black Sea Fleet to hunt for the Arctic Sea, telling commanders to take all necessary measures to find and free the vessel.

It was intercepted by the anti-submarine ship Ladny on August 17 near Cape Verde, off the West African coast, about 2,500 miles off course.

Eight men are in custody accused of piracy and kidnapping. The Foreign Ministry has described them as two Russian citizens, one Latvian, one Estonian and four stateless persons.

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