The raids at Peter Boddy Licensed Slaughterhouse in Todmorden, West Yorkshire, and Farmbox Meats in Llandre, Aberystwyth, took place yesterday.
The FSA said the Yorkshire slaughterhouse had supplied horse carcases to the Welsh processor, and that investigators were "looking into the circumstances through which meat products, purporting to be beef for kebabs and burgers, were sold when they were in fact horse."
Meat and paperwork including customer lists were seized at both sites. The FSA has also suspended operations at the plants while investigations continue.
This is the first time a UK slaughterhouse has been implicated in the horsemeat scandal, with previous leads suggesting that the contaminated meat was coming from European suppliers.
Andrew Rhodes, FSA director of operations, said: “I ordered an audit of all horse-producing abattoirs in the UK after this issue first arose last month and I was shocked to uncover what appears to be a blatant misleading of consumers.”
Environment secretary Owen Paterson said the revelation that UK businesses might be knowingly selling mislabelled meat was “absolutely shocking”.
“It’s totally unacceptable if any business in the UK is defrauding the public by passing off horsemeat as beef. I expect the full force of the law to be brought down on anyone involved in this kind of activity,” he said.
Peter Boddy, the owner of the West Yorkshire slaughterhouse, told ITV that he was co-operating with officials, while a spokesperson from Farmbox Meats denied any wrongdoing to BBC reporters.
The results of the first round of UK industry testing on processed beef products are due on Friday (15 February). Rhodes told the BBC this morning that the FSA’s investigations into the scandal would be “relentless”, and that the Agency would continue until “there was nothing left to find”.
Ministers from France, Ireland, Britain, Romania, Poland, Luxembourg and the Netherlands are due to meet in Brussels tonight to discuss the scandal.