MAFF said nearly 30 per cent of cases confirmed by vets in the field - around 450 of the 1,573 so far confirmed - did not prove positive when blood tests were carried out at Pirbright, Surrey, the world’s leading foot-and-mouth laboratory.

In addition, of the 250 cases where animals were slaughtered on suspicion of having the disease, only 46 cases (18.4 per cent) were later confirmed positive by laboratory tests.

That raised the possibility that hundreds of farms were wrongly diagnosed, leading to the unnecessary slaughter of many thousands of animals on those farms and on hundreds more surrounding farms. The tests for foot-and-mouth at Pirbright are considered highly effective by scientists, but a MAFF spokesman said negative results did not necessarily mean foot-and-mouth was not present on the farms.

It could have been that the animals were not in the stage of the disease where the virus would show up in tests, he said.

MAFF also said speed of slaughter had been crucial in the fight against foot-and-mouth and vets diagnosing animals in the field could not wait for laboratory results before moving to slaughter.

But the figures, revealed by senior vets, will fuel anger among farmers who feel their healthy animals were slaughtered for no reason.

If the farms were misdiagnosed, the mistakes will also have cost the taxpayer millions of pounds in compensation.

Senior vice president of the British Veterinary Association Andrew Scott said most vets had not seen a case of foot-and-mouth disease before.

"I think that that’s been a problem too and as the disease progressed and more experienced veterinary surgeons were recruited into the system then diagnosis probably became more accurate," he said.

"At the time, once the decision not to vaccinate had been taken, when we were running at 40 cases a day and the accent was on getting animals killed quickly, the only way to do that was to kill and then see where you were afterwards."

Last night MAFF said: "We have acted on the best scientific advice throughout.

"Speed of slaughter is crucial to successful control and eradication of the disease.

"Waiting for test results to come through before taking action would risk not bringing the outbreak under control.

"In order to ensure the necessary speed is achieved, confirmation of disease can be decided on clinical diagnosis by a vet in the field in consultation with Page Street (MAFF's foot-and-mouth control team) - laboratory tests on these cases are positive in more than 70 per cent."

Meanwhile, the Scottish executive gave a clear hint yesterday that a slaughter policy will never be used again.

Winding up a debate on how foot-and-mouth had devastated Dumfries and Galloway, rural development minister Ross Finnie told parliament that treatment of the disease had to be looked at afresh, with money invested in vaccine research.

He said: "The present range of vaccines available do not answer the question of control. But in the 21st century there simply has to be another way of handling a disease like this."

Ironically, his statement came on the day the executive confirmed its hard-line slaughter-to-eradicate policy, when the owner of Mossburn animal sanctuary lost her appeal. [She won it eventually, as you can read here] Mike Russell, SNP, intervening, told Mr Finnie that there was cross-party support for the way he had handled the crisis, but there was huge public disquiet about incidents such as the animal sanctuary.

Mr Finnie said the present epidemic had been dealt with at all times on the best scientific advice. At no stage had animal lives or farmers' livelihoods been "recklessly sacrificed".

Animals slaughtered had not been, as claimed, disease free, but a risk to other animals.

That statement was made as a fifth successive disease-free day was confirmed for Scotland. There have been only two in the past nine days as the UK total has crept to 1,570.

But as Elaine Murray, the MSP for Dumfries, pointed out in the debate she had initiated, of the 182 confirmed cases in Scotland almost all have been in Dumfries and Galloway and a further 1,300 farms have had livestock slaughtered in the contiguous and 3km culls.

More than 60,000 cattle and 500,000 sheep, average losses of £22,000 for hundreds of small businesses and lost jobs were the price the region had already paid for saving most of Scotland from the disease, she said.

She welcomed the further package of assistance measures to assist areas worst affected by foot- and- mouth announced by Mr Finnie yesterday.

But she added that more was needed and that every other possible source of funding to help a region in economic crisis must be considered, including Lottery money.

The executive’s extra funds included a payment to Dumfries and Galloway Council of £2 million "on account" to pay for costs incurred in controlling the disease and additional funds of £5 million, out of Scottish Enterprise's existing budget.

South of Scotland Conservative MSPs David Mundell and Alex Fergusson said that Mr Finnie's announcement of help could only be a start.