Russia's foreign minister said the circumstances of the ship's disappearance would become clear in due course.
The Maltese-registered Arctic Sea was officially carrying timber from Finland to Algeria when it was boarded on July 24 by a group of 8 men. They were charged with kidnapping and piracy after it was intercepted by Russian warships off Cape Verde.
Since then there has been speculation that the ship, manned by a crew of Russians, Estonians and Latvians, was carrying a secret cargo.
Media reports over the weekend, citing military sources in Israel and Russia, said the Arctic Sea had been loaded with S-300 missiles at the naval port of Kaliningrad without the Kremlin's knowledge. Mossad, Israel's intelligence service, had been monitoring and tipped off Moscow.
Speaking to reporters, Russian Foreign Minister Sergei Lavrov dismissed the reports: "This is absolutely not true."
The truck-mounted S-300PMU1, known in the West as the SA-20, can shoot down cruise missiles and aircraft. It can fire at targets up to 150 km (90 miles) away and can travel at more than 2 km per second, according to Russian media.
The advanced anti-aircraft system have been a sore point in relations between Moscow and the Jewish state, which has lobbied Russia to pull away from selling them to Iran, saying they could protect Iranian nuclear facilities against air strikes.
ALL WILL BECOME TRANSPARENT
Russia has repeatedly denied claims arms were on the 97-meter (318 ft), 4,000 dwt ship. Media reports claimed the Kremlin had ordered a rescue mission aboard the ship to avoid an international embarrassment surrounding a secret cargo.
"All will become transparent, and I hope that everyone will be convinced that the rumors you refer to are absolutely groundless," Lavrov said.
Russian investigators on Tuesday later said they had so far found nothing aboard the Arctic Sea apart from materials that should be on board, Interfax news agency reported.
Russian maritime expert Mikhail Voitenko caused an international storm when he said the ship could be carrying illegal weapons. The editor of Russia's respected Sovfracht maritime journal, Voitenko fled to Istanbul last week after he received anonymous threats and the magazine later sacked him.
Charges of kidnapping and piracy were brought against eight crew members two weeks ago in Moscow. Their lawyers called them "peaceful ecologists"
Russian prosecutors maintained the ship was carrying timber.
Assumed to have the region's only atomic arsenal, Israel supports U.S.-led diplomatic efforts to deny Iran the means of making a nuclear bomb. But Israel has hinted it could use force in a standoff that has often pitted Western powers against Russia.
(Reporting by Amie Ferris-Rotman)
