The results came after eight weeks of DNA testing on more than 4,000 beefs products, of which 193 were positive for horse.
The Commission also found that 0.5% of the 3,000 tested horse carcasses contained traces of phenylbutazone, known as bute, a potentially harmful drug which is banned from entering the human food chain.
Ahead of the publication of the results, the European Food Safety Authority (EFSA) released a statement saying the bute residues were of low concern for consumers. There was also no evidence that eating horsemeat poses a health risk, it said.
"Today's findings have confirmed that this is a matter of food fraud and not of food safety," said Health and Consumer Affairs Commissioner Tonio Borg.
The tests were carried out at retail level on products marketed as beef and in horsemeat abattoirs to test for bute, for which the EU executive provided 75% of the funding.
The horsemeat scandal has become a priority for Borg after polls showed that it hit consumer confidence in the food industry as well as sales of ready meals.
The Commission said that it would release proposals to tighten up controls in the food production line in a drive to combat instances of fraud.
"In the coming months, the Commission will propose to strengthen the controls along the food chain in line with lessons learned," Borg said.
The tests showed that France had the most cases of illegal horsemeat of any EU country, with 47 of the 353 tests carried out in the country resulting positive for horse, a rate of more than 13%.
"In terms of image it's not good. It risks delaying our attempt to regain consumer confidence to get out of the crisis, because it is not over yet," Jean-Rene Buisson, chairman of the French food industry group ANIA, told Reuters news agency.
The UK had the most cases of bute, with 14 positive tests in horsemeat destined for human consumption.
The only other countries to find bute in horsemeat were Ireland and the Czech Republic, each recording a single positive result.
"The bute is now really concentrated in the UK, but mainly because the UK has tested every horse slaughtered since February, so they have done a huge number of tests - more than 800," said a senior EU source who spoke on condition of anonymity.