The suspected case of BSE on a Co Louth farm is likely to see Ireland's international beef-status downgraded.
The disease was identified in a five-year-old dairy cow which was imported into the country.
The revelation comes a week after the World Health Organisation officially recognised Ireland as having a "negligible risk" for BSE.
However, the status will "in all likelihood" be downgraded to "controlled risk" after it was confirmed that there was a suspected case of Bovine Spongiform Encephalopathy, the first here since 2013.
The animal was tested this week and the results became known on Wednesday evening.
Agriculture Minister Simon Coveney said it was an "isolated incident" and there was no risk to people.
"It is unfortunate that the OIE (World Organisation for Animal Health) last week put Ireland on clear status as regards our beef after 11 years of being seen as a controlled risk, and in all likelihood that will revert once again," Mr Coveney said.
He made reassurances that Ireland's beef trade should not be affected.
Mr Coveney said it "should make no difference to our trade partners who have been contacted and reassured that the situation is in hand".
"There is zero risk to humans in this case, the system we have in Ireland means this animal could never have found its way into the food chain," he told RTE Radio today.
Mr Coveney added that the cow had three calves, which have been placed in quarantine and will be destroyed.
The most likely way in which BSE - commonly known as Mad Cow disease - was contracted was through feed.
It will take at least a week to confirm the case, with Simon Coveney saying "we are anxious to understand how this happened, and when we have conclusions we'll be open about this.
"It's not confirmed and it won't be confirmed for another week or so," he said.
"We're satisfied that the likelihood here of BSE is such in this one animal that we need to officially issue a statement on it," he added.