McColgan Quality Foods Ltd in Co Tyrone is a properly certified supplier of Halal food - which is food deemed acceptable to Muslims, who are barred from eating certain products including pork.
"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," a spokesman said.
"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."
It is understood McColgan Quality Foods supplied Halal products to only one distributor, a company called 3663, and no prisons in Northern Ireland were affected.
No other McColgan products are subject to any official investigation at this time.
Food distributor 3663, which has been suspended as the supplier to the Ministry of Defence, expressed shock and said the situation was "wholly unacceptable".
It also confirmed that all Halal products from the supplier have been withdrawn.
This is not a matter of dietary preference, but of Islamic law. There are clear hospital and prison rules that Halal meat must be on the menu.
Juliet Lyon, Prison Reform Trust
"3663 would like to clarify that the very small number of Halal savoury beef pastry products that have been withdrawn from supply were only ever distributed to custodial establishments," a statement said.
McColgan Quality Foods Ltd counts supermarket chains Lidl, Nisa, Spar and Costcutter among its customers.
Testing of the savoury beef pastry products at the centre of the scandal was undertaken by 3663 as a precaution, in the wake of horse meant being found in burgers.
The distributor recognised a potential connection between a Halal beef producer mentioned within the Food Safety Authority of Ireland report and a supplier of Halal savoury beef pastry products stocked for the MoJ.
The MoJ was informed of the situation and the products were quarantined pending DNA testing.
The distributor has said it will not source any further Halal products from McColgan Quality Foods.
"Our sentiments echo those of the Ministry of Justice in that this is a wholly unacceptable situation and one that we deeply regret," 3663 said.
"We are, however, relieved that our own prompt actions following identifying a potential risk from the FSAI report enabled the earliest possible removal of these products from sale."
It is the responsibility of food businesses to ensure the food they sell contains what it says on the label.
Food Standards Agency
Justice Minister Jeremy Wright said: "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."
The revelation comes after the Silvercrest plant in Co Monaghan was dropped as a supplier to Burger King, Tesco, Aldi and the Co-Operation Group, over burgers contaminated with horse DNA.
Irish Agriculture Minister Simon Coveney has claimed suppliers in Poland were the likely source of the contaminated meat.
The Food Standards Agency has called an urgent meeting of major retailers and suppliers on Monday to "ensure that everyone is fully aware of their responsibilities".
A spokesperson added: "This is an unacceptable situation and people have a right to expect that the food they are eating is correctly described.
"We are considering, with the local authority, whether legal action is appropriate following the investigation."
Local representatives of the food industry will also meet in Belfast on Monday as part of the UK investigation.