The company which supplied halal food found to contain traces of pork DNA has removed all products from the manufacturer.
Food distributor 3663 carried out its own tests after initially fearing five of its halal products may have contained horse meat. But tests found it was pork DNA traces.
A 3663 spokeswoman told the BBC the company was "shocked" at the findings of the tests.
The Ministry of Justice (MoJ) has suspended 3663 - a supplier of meat to prisons - after discovering that food products may contain traces of non-halal meat, despite being sourced from a properly halal-certified supplier.
Islamic law forbids the consumption of pork. All the contaminated products have been withdrawn, the MoJ confirmed. 3663 said in a statement its sentiments echoed those of the MoJ, and said it was a situation that "we deeply regret".
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) was immediately informed before steps were taken to suspend the relevant supplier.
The FSA said the local authority where the supplier is based is now investigating how the contamination came about, and whether products have been distributed elsewhere in the UK.
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."
The Prison Reform Trust said it welcomed the immediate apology and investigation. Its director Juliet Lyon 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."