The North's Department of Agriculture has confirmed the second case of foot-and-mouth disease there.
While the preliminary sample sent from a farm in Ardboe, Co Tyrone, to the Pirbright Laboratory in Surrey on Wednesday had proved negative, a second tissue sample was confirmed as positive last night.
Pirbright reported to the Agriculture Minister, Ms Brid Rodgers, that it had isolated the FMD virus from cattle on the farm of Mr Paddy Donnelly.
In a statement, Ms Rodgers said: "This is terribly disappointing after the good news we had yesterday. We cannot take any chances with FMD and on the evidence from the laboratory, we must now regard this as a positive case.
"I want to re-enforce my advice to all farmers that this case is now to be regarded as the second outbreak of foot-and-mouth disease in Northern Ireland and I urge them to be as vigilant as possible."
Northern Ireland had managed to secure European Union support for the resumption of meat exports but there were fears last night that the ban would be reimposed.
There was devastation among farmers' organisations at the news. Mr Michael McCoy from the Northern Ireland Agricultural Producers' Association said he was "absolutely dismayed" that 41 days since the first outbreak in Meigh, Co Armagh, there was now a second case.
"This is a disaster. Farmers over the last couple of days and nights have breathed a great sigh of relief. They just can't take it in. What's happened? How come in one instant we are told `no, it's not a case of foot-and- mouth and less then 36 hours later we are left with a situation where people don't know which way to turn. It's a terrible situation."
Mr Joe O'Donnell from the Ulster Farmers' Union said: "Our thoughts are with the farming family and the farming community involved. The whole farming community on hearing this news would just urge people to be totally vigilant at this stage and co-operate fully with the Department of Agriculture."
The UFU president, Mr Douglas Rowe, said his heart went out to the Donnelly family and their neighbours. "It is heartbreaking for the family but it is also heartbreaking for the farming industry that there is an outbreak bang in the middle of the country. We have lost our regionalisation status and we are now back fighting the disease again." A spokeswoman for the Northern Irish Tourist Board said the industry was very concerned about the new outbreak.
"At this stage our advice to visitors is that they are welcome to Northern Ireland but we would urge them to comply with the restrictions that are in place for everyone."
Mr Martin McGuinness, MP for the mid-Ulster area - in which the farm is located - said his reaction was one of "great shock and bitter disappointment".
"This is the gravest situation imaginable for the whole island. We will spare no cost in our efforts to combat this terrible threat to our farming community and the whole agricultural industry."
The Democratic Unionist leader, the Rev Ian Paisley, who chairs The Assembly Agriculture Committee at Stormont, is seeking to recall his colleagues to discuss the latest developments early next week.
The DUP leader was reported to be "very upset and alarmed" at events and in particular the confusion surrounding the test results at Ardboe.
An SDLP councillor in the area, Patsy McGlone, said the farming community in Ardboe was going through a range of emotions following tonight's announcement.
An SDLP councillor for the area, Mr Patsy McGlone, who had been in touch with the Donnelly family not long after the herd started showing the symptoms of the disease, said: "This could not have been worse for people in this area.
"There is despondency, doom, a sense of loss, fear about the future - all those emotions - because people are aware of the trauma that the Donnellys are going through and of the wider implications for them."