Highly classified intelligence documents relating to two of the most sensitive issues involving Britain's security interests - al-Qaida in Pakistan and the situation in Iraq - have been found on a train near London, it was disclosed last night.

The documents, including one marked Top Secret, are believed to be detailed and up-to-date assessments by Whitehall's Joint Intelligence Committee (JIC).

They were found on Tuesday and handed to the BBC's security correspondent, Frank Gardner, who reported the loss. The BBC said the documents were left on the train by a senior intelligence officer.

A Cabinet Office spokesman said last night that the documents' high security classification meant they would have had a limited circulation. "There has been a security breach, the Metropolitan police are carrying out an investigation."

A Scotland Yard spokesperson said its counter terrorism squad would be heading the investigation. "We can confirm that we are making inquiries in connection with the loss of the documents."

Gardner said the documents were left in an orange cardboard envelope on a train from London Waterloo to Surrey by a "very senior intelligence official" working in the Cabinet Office. A police search was launched when it was realised that they were missing, as officials were concerned at the possibility of such sensitive papers getting into the wrong hands, he said.

The envelope was picked up by a fellow passenger, who found a seven-page document inside setting out the latest government assessment on the Islamist terror network al-Qaida, along with a "top secret and in some cases damning" assessment of Iraq's security forces, said Gardner.

The al-Qaida document, commissioned jointly by the Foreign Office and the Home Office, was classified "UK top secret", he said. Each page was numbered and marked: "For UK, US, Canadian and Australian eyes only." The 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 taken out."

The BBC said the two reports were JIC assessments. A British intelligence assessment of the strength of al-Qaida in Pakistan would be sensitive and potentially damaging if read either by hostile interests or the Pakistan government. An assessment of the efficiency of the Iraqi security forces could be embarrassing if seen by the Iraqi government or insurgents.

The intelligence officer had permission to take the documents out of the office as long as sufficient security was provided, meaning a locked box, Whitehall officials said.

The fact that the investigation is in the hands of the police rather than MI5 suggests the documents were lost or mislaid and the official had not been targeted. The officer was still at work, Whitehall sources said. The loss is the latest in a string of recent data security lapses.