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The National Audit Office has launched a new inquiry into the foot and mouth epidemic, amid fears that the Government has not learned the lessons of the disaster.

The powerful Parliamentary watchdog confirmed yesterday it had started a fresh investigation to establish what steps the Government had taken to avoid a repeat of the 2001 disaster, which led to the slaughter of six million animals and landed the taxpayer with a 3 billion bill.

A spokesman said: "Our study will follow-up the recommendations made in the Public Accounts Committee's highly critical report of 2002 and the government's response of May 2003.

"The report will examine the steps taken to reduce the chances of another large-scale outbreak; arrangements designed to improve disease control should another outbreak occur; and the steps taken to reduce the cost of future outbreaks."

Last year the WMN revealed the European Commission was set to withhold hundreds of millions of pounds due to the UK because of the Government's mishandling of the disaster. Normally, the UK would be entitled to 60 per cent of the costs of a disease outbreak from the Commission. The Government submitted a claim for 1.6 billion, but European auditors are believed to be unhappy about paying more than half the bill - with the result that the UK could lose 800 million - because of ministers' failure to control costs.

In a statement, the NAO confirmed that "the European Commission intends to disallow a substantial proportion of the compensation".

This issue is also likely to form part of the new inquiry.

News of the fresh investigation emerged as a senior civil servant defended the Government's original foot and mouth inquiry.

Sir Brian Bender, the top civil servant at the Department of the Environment, Food and Rural Affairs, told MPs that it would have been "deplorable" if any ministers or officials had been singled out for criticism over the disastrous series of events.

Sir Brian, who was also permanent secretary at the former Ministry of Agriculture Fisheries and Food at the time of the crisis, said: "Identifying who was to blame and trying to nail people was not the intention of ministers. I deplore the tendency to try to finger people rather than learn the lessons."

Sir Brian also defended the decision to hold the bulk of the official "lessons learned" inquiry in secret.

He said that the decision, which was taken by Tony Blair, was designed to produce "forward-looking" recommendations quickly. But he said taking evidence in private might also have helped to "contribute to greater candour" from witnesses.

Several MPs on the Commons public administration committee expressed concern about the practice of taking evidence in private except where strictly necessary.

Ian Liddell-Grainger, Conservative MP for Bridgwater, said the "lessons learned" in the inquiry had failed to convince a large section of the rural community that the full truth about the handling of the disaster had been uncovered.

He added: "This was a disaster for the nation that affected hundreds of thousands of people. Surely we should have had some form of very public process to give people confidence that we had got to the truth."

Labour MP Gordon Prentice also noted that "huge numbers of people out there were clamouring for a public inquiry".

The Chief Medical Officer Sir Liam Donaldson, who was also giving evidence to MPs yesterday, said that although private inquiries had some advantages they were becoming "increasingly difficult to sustain" because the public did not trust them.

He added: "The trouble is it always sounds very bad to say you are not going to have a public inquiry because it sounds as if you are trying to withhold things."

Last night, Owen Paterson, the Shadow Minister for Agriculture, said he welcomed the NAO's decision to open a new inquiry "very enthusiastically". He said he had repeatedly made the point that the government had consistently failed to establish where and how the FMD outbreak started.

"We are today wide open to another outbreak of foot and mouth because we just don't know where the disease actually came from and how it got to Bobby Waugh's farm. The Lessons Learned Inquiry never established how it got there," he said. "We do not know where the disease actually originated from."

Mr Paterson said he had just viewed a video taken by Northumberland County Council of Bobby Waugh's pig farm, which has been blamed as the source of the outbreak in some quarters.

He described the conditions there as "abominable" but said it was never proved how the disease had reached the farm. He said he had yesterday tabled parliamentary questions on the subject seeking further efforts to positively determine the source of the outbreak.

"The outbreak of foot and mouth and the way it was dealt with represents one of the most appalling cases of misgovernment since the Second World War," he said.