Dr Paul Kitching, one of the leading experts on the disease, discloses in an internal memo that one in four farms has been wrongly diagnosed as infected.

This means that, when the culls on neighbouring farms are taken into account, about 550,000 of the 2.2m animals killed to date have been unnecessarily slaughtered.

Kitching's memo discloses that "it is important to note that at least 25% of the [animal] samples submitted from infected premises are not registering as positives". Some 400 of the 1,600 farms condemned as infected are now known never to have had the disease.

The five-page leaked memo - a summary by the National Sheep Association of a meeting it held with Kitching - is an indictment of the government's foot and mouth failures.

Kitching is leaving his post as head of the exotic diseases department at the Institute of Animal Health in Pirbright, Surrey, the official foot and mouth research centre, for a job in Canada. He sits on the committee set up to handle the crisis, and this weekend backed calls for a public inquiry into it.

He believes the policy of culling within 3km of an infected farm was based on the wrong model and was introduced on the back of a "fundamentally flawed" prediction. The models developed by the Ministry of Agriculture, Fisheries and Food (Maff) were based on the 1967 epidemic, which affected pigs and cattle. Kitching's memo stated they failed to take into account that this year's outbreak hit mainly sheep, which are not as infectious. "The different reactions to the disease between species had not been taken account of."

The memo reveals for the first time how civil servants and scientists blundered in trying to predict the spread of the disease. As a result, Maff targeted resources in the wrong areas.

Kitching's colleagues said that he was embarrassed at the way the crisis had been handled by Downing Street.