It is the first time that the ministry has been forced to take such action and was said by the National Farmers' Union to set "an unwelcome precedent". The smallholders had objected to their sheep, some of which were pedigree stock and rare breeds, being included in the blanket cull of more than 45,000 in south Anglesey after 13 suspected cases were found.

Fiona Cowie, a biology lecturer at Bangor College on the mainland, had objected to the inclusion of the five organically-reared sheep and eight lambs she keeps for her own consumption on five acres at Brynsiencyn, within the blanket cull zone.

"The whole thing became about more than five sheep. It became a matter of principle. I'm a scientist. I'm not a numbskull in a cloth cap. I was just trying to get some good scientific reasons for this cull."

Funded by an anonymous benefactor, who contacted them via their solicitors, the five argued in court that they should be allowed to have their sheep tested instead of being culled. "I just asked for blood testing as I thought that the animals in this corner of the island were free of the disease."

Miss Cowie, 40, accused the ministry and the Welsh Assembly of "anomalies and poor science" in devising the area of the cull. "The cull covered this entire part of Anglesey. They took a line to the left of the road and slaughtered everything.

"They haven't done that anywhere else in Britain. We are 2.5 kilometres away from the nearest case. Yet 250 metres from the first case you can see sheep grazing normally. They took the sheep and left the goats in the cull area, even on contiguous farms.

"I had a friend who was begging them to do the goats too as she thought they were infected. They gave some exemptions, but they would take 45 sheep and leave 15. Everyone has said that's just stupid. This is what I've been battling against."

Einir Davis, who has 17 sheep and an orphan lamb, said last night: "We're overcome. We can't believe we've got them to back down." Toni Lowe, who has 60 pedigree Lleyn sheep, said: "I'm not some dotty old lady with a few pets. These animals are breeding ewes. The science was all wrong. They were clean, they didn't need to be culled. Maff has gone mad with its culling, it's killing everything in sight."

A ministry spokesman said: "Because of the location of the sheep some considerable way from susceptible animals these sheep are unlikely to be in danger of foot and mouth and we have concluded that it is not appropriate to press for slaughter. We will continue to monitor the situation."

A NFU spokesman said "There have been many farmers on the island who have had to sacrifice their livestock for the good of farmers elsewhere. We don't understand why these people should be excluded from that."