The testing was recommended because of the potential presence of an anti-inflammatory compound given to horses, phenythbutazone, which could endanger the health of people who eat the flesh, the EUobserver reported Thursday.
Health commissioner Tonio Borg said member states would test 4,000 samples of horsemeat from slaughterhouses and 2,500 samples of processed beef products.
The tests will begin this month, with preliminary findings to be released April 15.
The controversy began last month when horsemeat from a French food processor was found in lasagna sold in British stores as containing all beef.
The processor, Spanghero, initially blamed slaughterhouses in Romania where the meat was purchased. Romania denied the allegations Wednesday, saying an investigation has found all the meat was properly labeled.
The EU signaled criminal behavior may be involved in the scandal, asking law enforcement agency Europol to coordinate information among member states, The Financial Times reported.
The scandal has also renewed calls for more stringent labeling of meat products.
The EU requires companies to label fresh beef with its country of origin, but processed foods have been exempted.
The commission attempted to extend the labeling requirement to processed foods in 2010, but the food and drink industry lobbied heavily against the proposal, saying ingredients came from too many places.
In light of the current crisis, the British Parliament has scheduled a special hearing for Monday.