As part of ongoing investigations into the horsemeat scandal facing the food industry, a quantity of frozen meat was detained from a cold store at the premises of Freeza Meats.
The Newry-based company is a specialist in burgers for the catering industry in Britain and Ireland.
The meat is potentially linked to that which was found in the Silvercrest factory in the Republic of Ireland last month.
"Of the 12 samples from the suspect consignment that have been tested, two of the samples came back positive for horsemeat, at around 80%," the FSA statement said.
"The investigation into the traceability of these raw materials and their source is underway. As this meat was detained, it has not entered the food chain."
Earlier it was revealed that horsemeat was found at a second meat processing factory in Co Monaghan.
Test results made public by the Irish department of Agriculture found that 75% equine DNA was traced in raw ingredient at Rangeland Foods in Castleblayney.
The investigation has shown that all implicated raw material ingredient is labelled as Polish product.
Irish department of Agriculture
The company, which supplies frozen beef burgers, employs 80 people and has a turnover of €18m.
Production has been suspended at the plant and the company has said that none of the product containing the horsemeat entered the food chain.
Rangeland is understood to have started enquiries after meat imported from Poland was blamed for the horsemeat found in burgers made at Silvercrest, part of the ABP Food Group, which is also based in Co Monaghan.
The company lost lucrative contacts with Tesco, Aldi, the Co-Op and Burger King because of the scandal.
Irish authorities are liaising with Polish officials and it is currently being investigated whether other Irish plants have used the polish meat.
Irish Agriculture Minister Simon Coveney has asked gardaí to join the investigation into the contamination.
"The investigation is focusing on the full supply chain including the meat trader concerned and others who facilitated the purchase of the product and its transfer to users in Ireland," the department said.
Meanwhile it was also revealed on Sunday that halal products designed for Muslim inmates in Britain, which were made by Co Tyrone firm McColgan Quality Foods, contained traces of pork DNA - the consumption of which is forbidden under Islamic law.