The rural affairs secretary, Margaret Beckett, has announced new arrangements to try to prevent the spread of foot-and-mouth disease through the movement of animals this autumn.
Areas like Devon, which are considered high risk, will be subjected to stricter controls than those free of the disease, or which have never been contaminated.
In Devon, farmers will not be allowed to move sheep in or out of the county, even though the area has seen no new cases for almost three months.
The decision has extensive animal welfare and financial implications.
Rural affairs secretary Margaret Beckett outlined details of the precautions at a news conference in London as the battle against the disease continues in many areas across the UK.
Mrs Beckett said the 'over-riding priority is to stamp out foot-and-mouth disease'. Autumn is usually the busiest time of year for the movement of livestock, but this year circumstances are far from normal.
She said: "This is not in any sense a perfect solution - there is no simple solution to any of these problems. It is a matter of balancing the different risks and tensions as best we can for all concerned."
The department has published a map detailing the foot- and-mouth status, county by county.
Devon was one of the worst-hit counties in the foot-and-mouth epidemic, with 173 separate cases out of the UK's total of 2,013 so far. The county was due to be declared foot-and-mouth free on Monday, the three month anniversary without a case.
But Government vets are being cautious following the reappearance of the disease in Northumberland after three months when no new cases were confirmed in the county. The Government is delaying granting disease free-status for Devon until more blood tests have been carried out on flocks. That could take at least until October. Defra says it hopes to have the extra flock testing completed by the end of the month.
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Lord Whitty, the Agriculture Minister, said it was necessary because of the high incidence of the disease in Devon at the height of the outbreak.
"A period of testing still needs to be completed. We hope that will be completed by early October, by which point Devon will be treated the same as other 'at risk' counties. But we are not yet in that situation and therefore some additional restrictions are required in Devon," said Lord Whitty.
It will mean more financial hardship for farmers and severe animal welfare problems with feed running short and livestock trapped outside as winter weather closes in.
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Anthony Gibson, regional director of the National Farmers' Union, said the new measures are not entirely unexpected.
"The very worst thing that could happen would be sheep harbouring the disease being moved and spread without anyone being aware they had the disease," he said.
"The measures for Devon are designed to pick up any undisclosed disease before those animals are moved thereby vastly reducing the threat that would pose."
There have been no new outbreaks of foot-and-mouth in Devon since the middle of June.
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