The Italian government has blocked an investigation into the whereabouts of a massive consignment of weapons removed from a military depot in the Mediterranean, amid speculation that the cargo was secretly supplied to Libya.

The weapons were from a consignment that included 30,000 Kalashnikov AK-47 automatic rifles, 32m rounds of ammunition, 5,000 Katyusha rockets, 400 Fagot wire-guided anti-tank missiles and some 11,000 other anti-tank weapons.

They were transferred from a store on the island of Santo Stefano, off the north coast of Sardinia, and transported to the mainland where they were loaded onto army trucks , a source familiar with the operation told the Guardian. But what happened to them after that is a mystery – and now a secret.

The arms were said to have been moved about a month after Silvio Berlusconi radically shifted his stance on Libya. Firmly allied to Colonel Muammar Gaddafi until the outbreak of hostilities, he was initially reluctant to do more than provide base facilities for France and Britain.

But on 26 April, after a telephone conversation with Barack Obama, he announced that Italian planes would join the air strikes on Libya in an attempt to break the deadlock on the ground. His announcement wrong-footed his coalition allies in the Northern League, who have repeatedly deplored Italy's subsequent involvement.

A prosecutor in the town of Tempio Pausania opened an investigation into the destination of the weapons but his inquiries were blocked by an order from the prime minister's office warning that the affair was covered by official secrecy, according to reports in two daily newspapers.

The prime minister's office was unable immediately to confirm or deny the report and the prosecutor's office in Tempio Pausania could not be reached for comment.

The weapons are understood to have been seized on board a ship intercepted by British and Italian warships at the mouth of the Adriatic during the Balkan wars of the 1990s. It emerged in subsequent court proceedings that the 19,400-ton Jadran Express was carrying enough weaponry to equip an army.

The ship, with a cargo of 47 containers supposedly packed with Egyptian cotton, was bound for the Croatian port of Rijeka when it was forced off course in an operation involving the British and Ukrainian intelligence services. Italian judges ordered the arms to be destroyed.

But they were instead moved to a munitions dump on Santo Stefano from where that the arms were reportedly removed between 18 and 20 May.

Not the least mystifying aspect of the operation is that the Italian navy used commercial ferries to transport the weapons.