The Department of Agriculture has identified a suspected case of BSE in Co Louth.
Tests are being carried out on a five-year-old cow found dead on a dairy farm in Co Louth.
The results due back in one week.
The animal in question was not presented for slaughter and did not enter the food chain.
If confirmed, it would be the first case of bovine spongiform encephalopathy (BSE), more commonly known as 'mad cow disease', in Ireland since 2013, when only one was confirmed.
There have not been more than 10 cases in one year since 2008.
Officials warned that if BSE is confirmed it may impact on Ireland’s beef and dairy industry recently being awarded the status of “negligible risk” and being downgraded to “controlled risk” by the World Organisation for Animal Health.
In the last year, Ireland was the first EU country to regain access to the US beef market and to have the beef ban lifted in China.
It is not clear how this case will hit the international trade deals.
The Department of Agriculture said officials were notifying national and international reference organisations and the European Commission.
“We have a full investigation underway already,” said Minister for Agriculture Simon Coveney.
“We haven’t had any new case of BSE since 2013 – so, for more than two years.
“So this is a surprise, but we’re dealing with it and we will get to the bottom of how it happened and of course we will reassure all of our trade partners that actually this is being dealt with in a very thorough and transparent way.”
Minister Coveney said he was hopeful the big international beef trade deals would not be at risk.
“There is absolutely no human risk here. This is an animal health issue,” he told RTE.
“Of course it’s important because of the reputational issue of the historic BSE problem that Ireland has dealt with in the past and the view among most people that BSE was a problem that was over for Irish agriculture.”
The Minister said it was fair to say this is an isolated case in a rare breed of cow, but accepted it was of concern.
He said tests would be done on other cows which may have shared the same feed as the dead cow and tracing will be done to establish if the animal had calves and they will be tested and possibly destroyed.
Minister Coveney revealed Ireland only secured the “negligible risk” status on its beef and dairy herds last week but that the big trade deals were agreed when Ireland still had “controlled risk” status.
“I’d be hopeful that actually people would see this as proof of a very robust testing system in Ireland,” he said.
Reports on BSE cases in Ireland show in 2013 there was one case, three in 2011 and 2012, two in 2010, nine in 2009 and 23 in 2008.
The disease was first diagnosed in cows in Ireland in 1989.
A link between BSE and the degenerative variant CJD was accepted in 2001 by the World Organisation for Animal Health.
It is believed to have spread into cattle herds via animal feed containing infected material, possibly offal that included brain or nervous system tissue from animals that died with the disease.
It is a fatal progressive neurodegenerative disease which can be transferred from animals to humans and was discovered in 1985.