The Ministry of Justice said it would withdraw the questionable meat from prison halal menus while the Food Standards Agency investigates the matter.
"This is an absolutely unacceptable situation and one which we regret greatly," Justice Minister Jeremy Wright said in a written statement. "Clearly this must be distressing for those affected and they can be reassured we are doing everything we can to resolve the situation."
Halal meat is meant to be free of pork in compliance with Muslim law. A test of meat used in pies and pasties labeled halal revealed traces of pork DNA.
The BBC said the halal investigation came after the discovery of horse meat sold in hamburger at British supermarket chains.
Critics of the FSA said the incidents were a sign the agency was too chummy with the industry it is supposed to regulate.