The three-month regime of checks - expected to be endorsed by the EU's Standing Committee on the Food Chain on Friday - will be launched in March with 2,500 random tests on processed food for horse DNA and 4,000 for bute. The results will be declared on April 15. The scale of DNA tests for April and May will be decided at a later date.
The ministers also agreed on tightening co-ordination between national authorities through Europol, the EU law enforcement agency based in The Hague whose normal remit is combating serious international crime and terrorism.
Earlier, Prime Minister David Cameron told the House of Commons that anyone involved in passing off horse meat as beef should face "the full intervention of the law", but insisted there was no evidence that products on the shelves of British shops were unsafe to eat.
Mr Paterson, meanwhile, hinted that investigations by UK food safety authorities may lead to further raids, following action at an abattoir in West Yorkshire and a Welsh processing plant on Tuesday.
He said that the raids, on the Peter Boddy slaughterhouse in Todmorden and meat processing plant Farmbox Meats at Llandre in Aberystwyth, followed methodical work by the Food Standards Agency, tracing back through the paperwork of companies where horse meat may be involved.