McColgan Quality Foods Ltd in Co Tyrone has been named as the source of the contaminated Halal beef pastry products, which were supplied by food distributor 3663 to prisons in England and Wales.
Tests found the products designed for Muslim inmates contained traces of pork DNA, the consumption of which is forbidden under Islamic law.
The company, which employs around 100 people, says it has withdrawn all products supplied to prisons while investigations are taking place. They said at no stage was pork a part of their recipes.
In a statement, the firm described the incident as "deeply regrettable".
Its contract has been suspended by the Prison Service.
Gerry McCurdy, from the Food Standards Agency, told UTV a meeting has been held with food businesses to remind them of their responsibilities in terms of producing food safely, hygienically and in terms of labelling.
He said that a thorough investigation is ongoing at the company premises to find out how the meat was contaminated.
"We are working with the local authority and the food industry, but I do have to emphasise we are not talking about food safety issues," he said.
"We are talking about composition and labelling and giving consumers information that they require.
"It's the food business operators' responsibility to ensure they comply with food law."
No other McColgan's products are subject to any official investigation at this time.
Food distributor 3663 expressed shock and said the situation was "wholly unacceptable".
"3663 would like to clarify that the very small number of Halal savoury beef pastry products that have been withdrawn from supply were only ever distributed to custodial establishments," a statement said.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 its products was undertaken by 3663 as a precaution, in the wake of the horsemeat burgers crisis.
The MoJ was informed of the situation and the products were quarantined pending DNA testing.