The controversial order to cull badgers in Wales was quashed by the Court of Appeal.
The Badger Trust appealed after a High Court judge upheld the Welsh Assembly government’s plans to trap and shoot badgers in west Wales.
It was among measures, including stricter controls on cattle, intended to eradicate bovine tuberculosis from north Pembrokeshire and neighbouring parts of Carmarthenshire and Ceredigion.
Lord Justice Pill said the Welsh Assembly was wrong to make an order for the whole of Wales when it consulted on the basis of an intensive action pilot area which only supported a cull on evidence within the IAPA.
The tuberculosis eradication (Wales) order was made in September last year to allow a non-selective cull of badgers in Wales.
Although the cull was supported by farming unions, a small number of landowners objected and there were clashes between protesters and contractors surveying badger setts.
Ministers insisted it was necessary to wipe out a disease which hit 42 per cent of cattle farms in the area in six years.
Lord Justice Pill said: “There is no doubt that farming is a very important part of the Welsh economy and that bovine TB is a particularly serious problem in Wales.”
He said the Badger Trust promoted conservation and welfare of badgers and the protection of their setts and habitats.
They were just as concerned about ways to tackle bovine TB and were not completely opposed to culls but only where it could be proved to be effective and that was not the case in Wales.
The appeal judge said Rural Affairs Minister Elin Jones was entitled to conclude that the evidence did demonstrate the chance of a substantial reduction in TB in livestock within the IAPA.
Lord Justice Pill said that, if the order had been confined to the IAPA in north Pembrokeshire, he would have dismissed the appeal.
The area was chosen because of a high incidence of the disease which was not true of other parts of Wales, he said.
“As countries go, Wales is a small country but there will be situations, of which this is one, where power devolved to the Welsh Assembly government will need to be exercised on a regional basis within Wales and not made subject to a single regime which applies throughout Wales.”
Ms Jones had said before the ruling that contractual arrangements were in place to start removing badgers if the court found in her favour.
She said: “We have evidence that there is a bovine TB reservoir in badgers in TB-endemic areas in Wales.
“I have also said repeatedly that there are no circumstances in which we would cull badgers across Wales in areas where there is no evidence that there is a bovine TB reservoir in wildlife.”