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The Metropolitan police has launched an investigation after top secret intelligence documents on al-Qaida and Iraq were left on a train in London, the Cabinet Office confirmed today.

It is understood the two documents, relating to al-Qaeda activity in Pakistan and the security situation in Iraq, were lost yesterday.

The files were left at Waterloo station, on a train heading to Surrey, by a senior security official. They were found by a passenger who handed them to the BBC’s security correspondent, Frank Gardner.

The documents, which were compiled by the government’s joint intelligence committee, contained the latest assessment of al-Qaida and a “top secret and, in some cases, damning” assessment of Iraq’s security forces, said Gardner.

A full-scale police inquiry was launched immediately as officials were concerned the sensitive papers could find their way into the wrong hands, he said.

The al-Qaida document, commissioned jointly by the Foreign Office and the Home Office, was classified “UK top secret”, said Gardener. It was so sensitive that each page was numbered and marked “For UK, US, Canadian and Australian eyes only”.

The second document, on Iraq, was commissioned by the Ministry of Defence.

Gardner said: “This was a clear breach of government rules. They should be sealed in a briefcase if they are taken out.”

A spokesman for the Cabinet Office said: “Two documents which are marked as ’secret’ were left on a train and have subsequently been handed to the BBC.

“There has been a security breach, the Metropolitan police are carrying out an investigation.”

The spokesman declined to discuss the contents of the documents, but said the papers had been in the possession of a senior intelligence officer based in the Cabinet Office.

Asked how many people would have had access to the papers, he said: “‘Secret’ is a high classification so they would have had limited circulation.”

A Met spokesman said: “We are making inquiries in connection with the loss of documents on June 10.”

The Conservative shadow security minister, Baroness Pauline Neville-Jones, attacked the government for its record of security lapses and called for an independent parliamentary inquiry.

“This is just the latest in a long line of serious breaches of security involving either the loss of data, documents or government laptops, further highlighting the most basic failures in this government’s ability to maintain our security.

“The government must make an immediate statement to parliament and an inquiry must be launched.”

The Liberal Democrat home affairs spokeman, Chris Huhne, said: “This is an appalling breach of security, which suggests that procedures on such sensitive matters are lax to the point of utter carelessness.

“There should be strict guidelines about when such secret documents are outside carefully monitored premises.

“It beggars belief that the government could have scored such a devastating own goal on the very day that it was pushing draconian counter terrorism laws through parliament.”

In January, the Ministry of Defence was forced to contact the security agencies MI5 and MI6, as well as banks and individuals, after the theft of a laptop computer from a car.

The computer held the personal details of 600,000 Royal Navy, Royal Marine and RAF recruits, and other people who applied to join the services.

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UPDATE:

The Cabinet Office has suspended the civil servant at the centre of an inquiry into the loss of top-secret documents on al-Qaeda and Iraq.

The unnamed Cabinet Office employee was questioned in an internal inquiry after the sensitive papers were left on the seat of a commuter train.