The Ministry of Justice has suspended a sub-contractor after it supplied halal food containing traces of pork DNA.
Distributors 3663 - which delivers halal items to the prison service - has withdrawn all halal pastry products provided by McColgan Quality Foods Limited.
The MoJ said 3663 had not been suspended, but that "sub-contractor" McColgan had.
A statement from 3663 said it had carried out its own tests on the products after initially fearing five of its halal products may have contained horsemeat. But tests found it was pork DNA traces.
The firm identified McColgan, a Northern Ireland-based company, as the source of "the very small number of Halal savoury beef pastry products" affected.
In a statement the company said: "3663 withdraws McColgan Quality Foods Limited halal pastry products from distribution to Ministry of Justice."
Islamic law forbids the consumption of pork.
On an Invest Northern Ireland-backed website, McColgan - based in Strabane, County Tyrone - is said to be "approved for the preparation of Halal product".
The website lists McColgan's customers to be popular supermarket brands including Lidl, Nisa, Spar and Costcutter.
It states McColgan's specialises in "a wide range of chilled & frozen, sweet & savoury convenience foods for retail and food service".
In a statement it said it was "proactively co-operating" with the Food Standards Agency.
"McColgan's has already taken swift measures to identify, isolate and withdraw all of the products which are supplied to The Prison Service while an investigation to determine the circumstances surrounding this deeply regrettable and unforeseen incident takes place.
"McColgan's is keen to stress that at no point has pork of any kind been included in the recipes of any of the halal-certified products it supplies."
The row comes after traces of horsemeat were found in burgers sold by some UK supermarkets, including Tesco.
3663 - the numbers in the name corresponding to the letters "FOOD" on a telephone number pad - said in a statement its sentiments echoed those of the Ministry of Justice, and said it was a situation that "we deeply regret".
It added that the beef pastry products were only distributed to prisons.
A spokesman for the MoJ said that following the discovery of non-halal meat and the traces of pork, all prisons were informed and the Food Standards Agency (FSA) immediately informed.
Justice minister Jeremy Wright said: "This is an absolutely unacceptable situation, and one which we regret greatly. Clearly this must be distressing for those affected and they can be reassured we are doing everything we can to resolve the situation. The Prison Service is investigating this as a matter of urgency."
On Thursday Burger King dropped the Irish food processing plant which supplied burgers contaminated with horse DNA.
The Silvercrest plant in Co Monaghan, part of the ABP Food Group, has lost contracts with the major fast food chain and also supermarkets Tesco, Aldi and the Co-operative Group.