A second set of secret government intelligence papers has been found on a commuter train, it was revealed last night.

The Treasury files included an assessment of the weaknesses in the trade and banking systems in Iran that would-be terrorists could exploit to finance weapons of mass destruction.

They also highlighted potential methods of terrorist funding, including how to defraud commercial websites and international payment systems, as well as outlining Britain’s policies on fighting global terrorist funding, drug trafficking and money laundering.

The documents were found by a commuter on a train bound for London’s Waterloo station on Wednesday and handed to The Independent on Sunday.

On the same day another set of secret files regarding the Al-Qaeda threat and Iraqi security forces was handed to the BBC. A senior intelligence official with the highest level of security clearance had left the papers on a train from Waterloo to Surrey last Tuesday.

The latest documents to come to light were prepared in advance of a global financial crime conference in London, bringing together members of the international Financial Action Task Force (FATF), which begins tomorrow.

The files include criticism of countries such as Iran, which have signed up to the FATF’s standards, and detail the weaknesses of the British HM Revenue and Customs’ IT systems, which track financial fraud.

Among the briefings were also draft speeches for senior British officials who are due to address FATF representatives at a reception at 11 Downing Street, on Wednesday.

Alistair Darling, the chancellor, who is in Japan for a G8 summit, has been told of the latest information breach and the Treasury last night insisted it would take action. “We are extremely concerned about what has happened and will be taking steps to ensure it doesn’t happen in the future,” a spokeswoman said.

The Cabinet Office civil servant who mislaid the documents that were handed to the BBC analysed data and provided reports for the Joint Intelligence Committee using information gathered by MI6, GCHQ and foreign intelligence services. He has been suspended.

The files, found in an orange cardboard envelope, included a seven-page report on Al-Qaeda “vulnerabilities” and refer to assessments of the terrorist group in Afghanistan and Pakistan. Each page was marked “For UK, US, Canadian and Australian eyes only”.

An investigation into the case by Sir David Omand, the former permanent secretary for intelligence and security, has been launched, and police are also looking into the matter.

However, Scotland Yard said last night that it was not involved in investigating the latest case.

Baroness Neville-Jones, the shadow security minister, said last night the government needed to “get a grip” on the issue of protecting sensitive data. “This is another incidence of the failure of the government to safeguard sensitive information and yet another example of a lapse in discipline,” she said.

“In this case, had the content been released, the potential consequences could have included prejudicing the UK’s position in international meetings – the government cannot allow this to continue.”

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