Police raided two British meat companies on Tuesday in their first action – jointly with food standards officials – into food fraud and the horsemeat scandal.

Officers entered Peter Boddy Licensed Slaughterhouse in Todmorden, West Yorkshire, and Farmbox Meats Ltd near Aberystwyth in Wales, as they investigated the circumstances in which horsemeat was sold as beef "for kebabs and burgers".

The Food Standards Agency said in a statement it believed Peter Boddy Licensed Slaughterhouse supplied horse carcasses to Farmbox Meats.

"The FSA has suspended operations at both these plants. Both West Yorkshire and Dyfed-Powys police have entered the premises with the FSA. The FSA has detained all meat found and seized paperwork, including customer lists from the two companies."

On Tuesday night the main entrance to the Todmorden abattoir, on a hillside above the town in West Yorkshire, was blocked by a tractor. Two people who appeared to be guarding the entrance refused to answer questions, and insisted journalists could not enter the grounds of the abattoir. Nearby farmers also refused to comment.

Andrew Rhodes, the FSA's director of operations, said he had ordered an audit of all abattoirs processing horses in Britain after this issue first arose last month. "I was shocked to uncover what appears to be a blatant misleading of consumers. I have suspended both plants immediately while our investigations continue."

The environment secretary, Owen Paterson, said: "This is 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."

Peter Boddy, the owner of the abattoir, said he will co-operate with FSA officers, denying they had "raided" his Todmorden premises. He said: "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."

He added that he does slaughter horses at his plant and that the meat is sold in Britain. One of the company's websites states that he has been "involved in agriculture and the meat trade for over 50 years".

It is the first time police have taken action in the scandal over mislabelling of processed beef products and came as the problems spread to the upmarket retailer Waitrose, which withdrew its Essential British Frozen Beef Meatballs after pork was detected in two batches.

They had been produced at an ABP Freshlink site in Scotland last summer. This plant, whose closure was announced last year, was not implicated in earlier horse or pork contamination scares at the Irish food group's Silvercrest and Dalepak sites, in Co. Monaghan, Ireland, and North Yorkshire respectively.

Waitrose said in a statement: "Several tests have been done on this product and, even though the results have been contradictory, we have taken the precautionary action of removing the frozen meatballs from sale and putting up customer information notices in all our branches."

The meatballs are safe to eat, but pork is not listed as an ingredient and should not be part of the recipe. The products Essential Waitrose Meatballs and 16 British Beef Meatballs 480g have a best-before date of the end of June 2013 and the end of August 2013.

Paterson held a second meeting in as many days with the FSA and food retailers and suppliers to discuss a new regime of random testing of foods.

He will travel to Brussels on Thursday to discuss the growing Europe-wide crisis with health and consumer commissioner Tonio Borg and his opposite numbers from France, Ireland and Romania.

Results of tests into the extent of contamination of beef products are expected on Friday. So far, several supermarkets have been forced to withdraw burgers, ready-made lasagne and bolognese, but the raids were the first to involve kebab meat.

"I would be appalled if these allegations are proven," said Alun Davies, the Welsh government minister for agriculture. His department was working closely with the Department for Environment, Food and Rural Affairs (Defra) and the FSA "to ensure this matter is dealt with swiftly and decisively", he added.

Mary Creagh MP, shadow environment secretary, said: "I welcome the action taken tonight by the FSA and the police. I'm glad the FSA has investigated the concerns about horsemeat entering the food chain I first raised with ministers three weeks ago.