The food safety watchdog has pledged a relentless investigation into allegations of horse meat being passed off as beef in the UK after two British plants were raided and shut down as part of the inquiry into the scandal.

Andrew Rhodes, Food Standards Agency (FSA) director of operations, said they would keep pursuing an investigation into a slaughterhouse in West Yorkshire and a meat processing plant in West Wales until there is "nothing left to find" after discovering evidence of apparent "blatant misleading of consumers".

"Our investigations have determined that we found horse meat that was produced at the plant in West Yorkshire being sent to a location in West Wales, a business called Farmbox," he told BBC Breakfast. "We entered that premises yesterday, FSA enforcement officers entered that premises, following up on the evidence that we found and we spoke to the staff there and we seized product and we found that horse meat had been used as though it were beef in kebabs and burgers at that premises."

His remarks were made after Peter Boddy slaughterhouse in Todmorden, West Yorkshire, and meat processing plant Farmbox Meats at Llandre in Aberystwyth, West Wales, had records seized and were temporarily shut down pending the outcome of investigations into claims they supplied and used horse carcasses in burgers and kebabs.

The FSA said it had "detained" all meat found at the premises and seized paperwork and customer lists from the two companies.

Asked if he was alleging that horse meat was passed off as beef, Mr Rhodes said: "That is absolutely right, yes. The Food Standards Agency is a science and evidence-led organisation and we don't do things lightly. We have very good evidence to support the actions that we have taken."

Slaughterhouse owner Peter Boddy said he would co-operate with FSA officers and claimed they had not "raided" his Todmorden premises. He told ITV: "It was not a raid - they are welcome to visit whenever they want. They just wanted to see my records, which I will be showing them."

Dafydd Raw Rees, of Farmbox Meats, told the BBC that the firm was licensed to deal with horses and it had been cutting horse meat, from the Irish Republic, for the last three weeks. "As far as I am concerned, I know nothing about the plant in West Yorkshire. I have never knowingly processed horse meat until three weeks ago," he said. "There is nothing we have done here which is not totally permissible."

Prime Minister David Cameron's official spokesman told reporters at a regular daily briefing: "As the Secretary of State has said, investigations are ongoing and we need to await the outcome of those, but it is totally unacceptable if businesses are defrauding the public. This results from the audit of horse abattoirs that the FSA began several weeks ago after the first evidence came to light of contamination."

Agriculture minister David Heath has met UK food retailers and suppliers to discuss the horsemeat issue.