The cargo ship allegedly hijacked by pirates amid claims that it was smuggling missiles to Iran has ended its three-month odyssey in Malta after being tested for nuclear contamination.

The Arctic Sea was allowed to enter the Grand Harbour in Valletta last night after the Maltese Civil Protection Department declared it free of radiation and chemical hazards. The Maltese-registered ship had been the focus of speculation that it was carrying Russian S300 advanced air-defence missiles to Iran.

Despite repeated promises to take it into port, the Russian Navy had held the Arctic Sea in international waters since seizing it from suspected pirates on August 17 off Cape Verde near West Africa, 2,500 miles (4,000km) off course.

The ship had been under guard by two Russian warships since then. An attempt to dock at Las Palmas in Grand Canary failed last month after disputes over the presence of Russian military officers. Algeria also refused to allow the Arctic Sea to enter its waters.

The ship was allegedly boarded by an armed gang two days after it left Finland on July 22 to deliver timber worth $1.7 million (£1 million) to Algeria. The Russian Investigative Committee released the Arctic Sea from a detention order on Wednesday after prosecutors insisted that they had found no evidence of suspicious cargo.

Nobody has explained why a ship transporting a relatively inexpensive load should have been the target of the first documented act of piracy in Northern European waters for centuries.

Solchart, the Finnish owners of the ship, calculated that the incident had cost the company more than €700,000 (£625,000) since the Russian Navy took control of the vessel.

A relief crew from Russia was in Malta to meet the Arctic Sea, which needs repairs. The captain and three crew members, who are all Russian, had been on board throughout the voyage. Their families complained in a letter to Vladimir Putin, the Russian Prime Minister, that they needed medical and psychological help.

It is unclear whether they will be free to return home to the Russian port of Archangel or be taken to Moscow for questioning.

Eleven other crewmen were held in Moscow for a week for interrogation by the Federal Security Service. They and the eight alleged pirates had been flown to Russia on three IL76 transport aircraft from Cape Verde, adding to speculation about a secret military cargo. The Russian aircraft are used to transport heavy weaponry.

The eight suspects, described as two Russian citizens, an Estonian, a Latvian and four stateless persons, are in custody in Moscow accused of piracy and kidnapping. They claimed to be ecologists who were rescued by the crew of the Arctic Sea when their inflatable dinghy got into trouble.

President Medvedev dispatched submarines and warships to find the Arctic Sea when it was declared missing. The Foreign Ministry later admitted that the ship’s movements had been tracked by Russian and Nato forces.

Suspicions about a cargo of smuggled missiles for Iran were strengthened when Binyamin Netanyahu, the Israeli Prime Minister, made a secret visit to Moscow last month for talks with Mr Medvedev and Mr Putin. The Kremlin and Israel initially denied that any visit had taken place, but later admitted that Mr Netanyahu had been in Russia.

Russian officials initially said that the Arctic Sea would be taken to the Russian port of Novorossiysk, but the ship remained at sea amid disagreements among the various governments involved and its owners.

The Ladny, a Russian naval vessel that had been accompanying the Arctic Sea, returned to its port last night. “The Russian Navy’s mission has been completed,” a Russian Defence Ministry spokesman said.

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