The precautionary cull of 2,500 sheep in south Armagh started late last night, safeguarding plans to allow the North to export meat and dairy products.
Farmers from the area around the foot-and-mouth outbreak in Meigh had earlier expressed concerns about the cull. These included how and where the animals would be killed and disposed of, and how much compensation would be paid.
Speaking after meeting the farmers yesterday, the North's Agriculture Minister, Mrs Brid Rodgers, said all their concerns had been met.
Farmers had been demanding compensation above the market price for the animals but the Minister said they had now agreed to accept full market value for every animal culled. If a farmer was not satisfied with the price awarded he would have access to independent assessors, the Minister said.
Mrs Rodgers denied unionist claims she had discussed immunity from prosecution for those who might have been involved in smuggling.
"The only thing I'm interested in is getting the sheep off the farm and getting them out of the way," she said.
"People make their claims, they're assessed, if everything is tallying then the subsidies are paid and if they're not then questions are asked. But that will be dealt with in the normal way."
The animals were to be collected from fields and brought to a warehouse in Newry, Co Armagh for slaughter. The warehouse is within both the 10kilometre exclusion zone and the "region" of Newry and Mourne.
A Department of Agriculture spokesman said all animals would be inspected before being transported to Newry. Only animals with visible symptoms of the disease are contagious, the spokesman said, adding that if any were found with symptoms further action would be taken.
From Newry the carcasses will be taken to a plant in the Duncrue area of the north Belfast docks and incinerated.