Random tests carried out by Northern Ireland’s Department of Agriculture have detected a higher incidence of BSE in cattle over 30 months of age.
Agriculture Minister Ms Brid Rogers said tests on 2,500 cattle, not destined for the food chain, identified 54 cases of the disease.
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The tests were carried out ahead of an EU-wide screening programme and were designed to help the North's case for a lifting on their beef exports to Europe.
Ms Rogers stressed the tests also revealed that animals under four years of age did not test positive for BSE, proving that measures to eradicate the disease introduced in 1996 were working.
"I want to stress that, while these results are disappointing, they are not entirely surprising. My department targeted the highest risk group of cattle - old sick animals," she added.
"None of them would have entered the food chain. Since this was a high risk sample, it should not be assumed that the level of BSE we found was representative of the overall picture."
Ulster Farmers' Union president Mr Douglas Rowe said the announcement was a disappointment, but they were determined to ensure the rigorous controls were recognised as the most stringent in Europe.
He added: "The safeguards in our local industry will continue to protect consumers and provide a blueprint for other European countries who are trying to match our controls.
"Incidents of sub-standard consignments of imported beef serve to highlight our strength and transparency."