Two plants in north London and another site in Hull were visited by officials from the watchdog who took away computers, documents and meat samples for tests and analysis.
The agency, which was involved in earlier raids at a meat-processing plant in Aberystwyth and at an abattoir in Todmorden, Yorkshire, targeted Dinos & Sons Continental Foods in Tottenham.
The other plants have not been named.
In a statement, the FSA said it had submitted a full file and evidence on this issue to Europol. It added: "The agency has continued to provide information to Europol, and this information has now been analysed by both Europol and law-enforcement agencies in 35 countries – across Europe and elsewhere."
A spokesman for Dinos & Sons said it was "co-operating with local trading standards officers".
He said: "There is no suggestion whatsoever Dinos & Sons' manufacturing processes have been compromised in any way,"
Calls have been made to speed up meat checks after horse DNA was found in meals delivered to schools in England and hospitals in Northern Ireland.
However, Rural Affairs Secretary Richard Lochhead made it clear rigorous tests carried out by companies supplying meals to schools, hospitals and prisons in Scotland had "confirmed to date they are clear of any mislabelled meat".
He added: "These detailed inspections continue to be carried out and I hope further reassurance can be offered in the coming days."
Most tests in Scotland will be completed next week.
Results published by the FSA showed that, of the 2501 tests carried out so far by retailers, 29 products had a positive reading for undeclared horse meat at or above a 1% level.
More than 950 tests are still in progress. The 29 results related to seven different beef products, all of which have been reported and withdrawn from sale.
As the results were published, Whitbread, one of Britain's largest pub and hotel groups, became the latest company to admit horse DNA had been found in its food, saying their meat lasagnes and beefburgers had been affected. The firm, which owns Premier Inn, Beefeater Grill and Brewers Fayre, said the products had been removed from menus.
Nigel Miller, president of the National Farmers Union Scotland said farmers "feel betrayed as well because in Scotland we've gone to such a huge effort to ensure everything is done right and traceability is total.
"To actually see retailers who are moving away to cheaper products and ignoring these very basic principles is just unbelievable."
The retailers' food tests showed cottage pie containing horse meat was sent to 47 schools in Lancashire. Local councillor Susie Charles explained few schools in the county used the product, which had been withdrawn.
She added: "Our priority is to provide absolute assurance that meals contain what the label says. Having discovered this one doesn't, we have no hesitation in removing it from menus."
In a separate development, it was discovered beefburgers containing horse meat were supplied to hospitals in Northern Ireland.
David Bingham from the NHS body, which provides meat for health trusts, said a range from a company in the Republic of Ireland had now been withdrawn.
He said: "We have acted immediately. As soon as we got information there may be a confidence issue, we withdrew the product."
A group of 11 food suppliers, including Tesco and Asda, yesterday issued a statement, saying they shared shoppers' "anger and outrage" and rejected criticism from Downing Street that they had "remained silent" during the crisis.
Peter Marks , chief executive of the Co-op, insisted the horsemeat scandal was a wake-up call for the food industry. He said: "It's our responsibility. We have to fix this and fix it quickly."
At Westminster, Owen Paterson, the UK Environment Secretary, said the test results showed the vast majority of products were clear of horse DNA.
He said: "Food businesses now have a lot of work to do. They need to move quickly to complete these tests and they need to show their customers they've taken the right steps to make sure this doesn't happen again."
However, Mary Creagh, his Labour shadow, said the public would be "shocked and dismayed horse meat has now been found in schools and hospitals" and called on David Cameron to "get a grip on this scandal now".
She added: "He should order the FSA to speed up its testing so that we have a full picture of just how far this has spread in our communities."
Justine Roberts of the parenting website Mumsnet echoed the call.
She said: "We are bemused at why schools and hospitals have been given until April to test the meat they serve while retailers and food companies were ordered to do it in a week."
Meanwhile, French meat processor Spanghero said it would disprove allegations the firm knowingly sold horse meat labelled as beef. French Consumer Affairs Minister Benoit Hamon had earlier said Spanghero was a likely culprit.
Dutch inspectors, too, began taking samples to discover whether shipments contained a drug given to some horses banned for animals intended for human consumption.
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