Police raided Peter Boddy slaughterhouse in Todmorden, Yorkshire, and Farmbox Meats in Aberystwyth, Wales, amid claims horsemeat was being put into the food chain as beef for kebabs and burgers.
Environment Secretary Owen Patterson said it would be totally unacceptable if any firm in the UK was involved and said he expected the full force of the law to be applied.
Yesterday there were further dramatic developments in the escalating crisis.
Waitrose became the latest store to withdraw a food range, this time beef meatballs, after tests revealed they might contain pork.
The supermarket, which has four Scottish branches, said tests on the 480g packs of 16 frozen Essential Waitrose Meatballs had been contradictory but it was removing them from sale as a precaution. It applies to packs labelled with best-before dates ending in June 2013 and August 2013.
Work at the Peter Boddy slaughterhouse and Farmbox Meats was suspended. Dafydd Raw Rees of Farmbox Meats said he had a licensed red meat cutting plant and had been in operation for three years. He said: "There is nothing we have done that is not totally permissible."
Andrew Rhodes, director of operations at the Food Standards Agency (FSA), 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."
Welsh Government Minister for Agriculture Alun Davies said: "I would be appalled if these allegations are proven."
Horse DNA had been discovered in raids on processing plants in Ireland and Yorkshire last month. The new raids shifted the recent focus from Europe.
Lamb ready-meals also came under scrutiny as a senior scientist warned they could be contaminated with horse DNA.
Dr Mark Woolfe, a former executive of the FSA, said: "If I was a retailer I would be looking carefully at my lamb products."
He also suggested the scandal had been triggered by a European decision to outlaw cheap British beef, known as disinsinewed meat (DSM). Mr Woolfe said the ban forced many to change from UK to foreign meat suppliers. The FSA insisted there was no evidence any lamb meals were affected.
Ministers from across Europe are to hold an emergency summit in Brussels today. On the agenda will be allegations organised crime is behind the contamination.
Tesco, frozen food firm Findus and Aldi removed certain foods after discovering they were supplied with products by French-based Comigel that contained horsemeat.
Labour accused the UK Government of failing to act on a list of affected suppliers. Mary Creagh, Shadow Environment Secretary, said: "It is not responsible to say to retailers, headteachers, and hospitals that they are responsible for the food they serve and not give them the information they need to identify where problems could lie." Downing Street said it was not aware of any such list. The Holyrood justice, education and health departments have been told to check their suppliers amid fears horsemeat could have been served in schools and hospitals.
Jim Walker, a former chairman of Quality Meat Scotland, called for the Irish meat processing sector to be cleaned up, claiming the country's low-cost horsemeat had created a temptation for others.
Meanwhile, the Scottish Government announced a £1 million campaign for Scotch beef to help develop new markets.
l The DNA technology used to identify Richard III and detect swine flu and foot-and-mouth disease is being modified to provide a "quality stamp" to be used in the current crisis. A version of the test is already used by Scots farmers to detect a bovine virus diarrhoea.