The Department of Education said the move was a precautionary step and the Food Standards Agency confirmed there is no health risk from the products.
"The Department has been advised that a supplier of frozen burgers to Education and Library Boards has instigated a full product recall following detection of trace amounts of equine DNA in the supply chain," said a Department of Education spokesman.
"This is a precautionary step and the Food Standards Agency has confirmed that there is no food safety or health risk from the products."
The department spokesman added that the position is "being kept under review".
The North Eastern Education and Library Board stopped serving burgers earlier this month, while they had recently been reinstated onto menus at the Southern Education and Library Board.
But the Department of Health confirmed burgers are currently not being offered at any schools across Northern Ireland.
Authorities in Britain and France are trying to trace the carcasses of six horses contaminated with phenylbutazone - or bute - which were slaughtered in a UK abattoir and may have entered the human food chain across the Channel.
The drug, which is potentially harmful to human health, was detected in eight horses out of 206 tested by the FSA in the first week of this month.
Two were intercepted and destroyed before leaving the slaughterhouse but the other six were sent to France, where horse meat is commonly eaten.
FSA chief executive Catherine Brown said the agency increased testing of horse carcasses over a three-month period last year after intelligence from abattoirs suggested bute was getting into the food chain.
Of 63 tested, four were found positive for the painkiller, prompting the FSA to start testing 100% of horse meat in January, which revealed the eight contaminated carcasses.
On Wednesday, European Commissioner for Health, Tonio Borg, proposed that EU members should carry out thousands of random tests for traces of horse, and bute, over a period of three months from March. The early results would be revealed in April.
It is expected the plan will be endorsed when it is put to a meeting of the EU's Standing Committee on the Food Chain.