The company which supplied halal food found to contain traces of pork DNA was named on Sunday.
Food distributor 3663 identified McColgan Quality Foods Limited, a Northern Ireland-based company, as the source of "the very small number of halal savoury beef pastry products" found to contain pork DNA which it supplied to prisons.
The statement said: "3663 would like to clarify that the very small number of halal savoury beef pastry products that have been withdrawn from supply were only ever distributed to custodial establishments.
All the pies in question have been withdrawn
"The products in question are from one particular food manufacturer, McColgan Quality Foods Limited, and have not been distributed to any other customer.
"All Halal products from this manufacturer have been withdrawn," the company said.
Islamic law forbids the consumption of pork.
3663 has not been suspended, but a "sub-contractor" has been suspended, the Ministry of Justice (MoJ) said.
3663 has said it was "shocked", and described as "wholly unacceptable" the discovery that some of the halal products it supplied were found to contain pork DNA due to McColgan Quality Foods being accredited by the Halal Food Authority.
According to buynifood.com, a website devoted to the produce of Northern Ireland, McColgan Quality Foods - based in Strabane, County Tyrone - is said to be "approved for the preparation of halal product".
The website lists among McColgan customers popular supermarket brands including Lidl, Nisa, Spar and Costcutter.
It states McColgan specialises in "a wide range of chilled & frozen, sweet & savoury convenience foods for retail and foodservice".
A spokesman for McColgan's said in a statement: "McColgan's can confirm that it is proactively co-operating with the Food Standards Agency and its local representatives following the discovery of trace elements of porcine DNA in a limited number of halal-certified pastry products which are supplied to 3663 as part of its contract to The Prison Service.
"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."
3663 - the numbers in the name corresponding to the letters "FOOD" on a telephone number pad - is currently contracted to distribute a wide range of products including ambient, frozen, fresh and chilled foods to the MoJ, all sourced from fully accredited and approved manufacturers and producers.
Following the horse meat scandal, 3663 recognised a potential connection between a halal beef producer mentioned within the FSAI (Food Safety Authority of Ireland) report and a supplier of halal savoury beef pastry products stocked for the MoJ.
3663 informed the MoJ of the potential connection as a precautionary measure, then took the decision that these halal savoury beef pastry products should be quarantined to prevent their use pending DNA testing.
3663 initiated DNA testing on multiple production batches of the halal savoury beef pastry products from McColgan and "disappointingly" received evidence that within the products tested there were traces of porcine protein.
The company has removed all halal products from McColgan from the supply chain and said it will not source any further halal products from the firm.
In the statement, 3663 said: "Our sentiments echo those of the Ministry of Justice in that this is a wholly unacceptable situation and one that we deeply regret.
"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."
Juliet Lyon, director of the Prison Reform Trust, said: "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.
"This lapse will have offended and distressed high numbers of Muslim prisoners and their families, so apologising, suspending the supplier and investigating the incident are the right steps for the Ministry of Justice to take."
The revelation follows the recent scandal over horsemeat contamination.
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.