Meeting in Luxembourg, EU 25 ministers gave a 'no qualified majority' to authorise Monsanto's NK603 maize, which has been modified to tolerate Monsanto's Roundup herbicide.
Last year a panel at the European Food Safety Authority (EFSA) declared that NK 603 was as safe as conventional maize.
"It is becoming more and more clear that the authorities in Europe are deeply divided over the subject of GM," said Friends of the Earth Europe's GM Campaigner Geert Ritsema.
Despite tough new rules to track and label genetically modified organisms enforced in April, food makers are opting to skip GM ingredients in European recipes because they are aware that the suspicious European consumer will not buy products containing such ingredients - a state of mind reflected by the divided ministers yesterday.
Failure by the ministers to reach a majority decision suggests Europe is still divided over the issue of biotech foods. The decision has now bounced back to the Commission for clearance. Industry observers suggest Brussels will give the go ahead, particularly in light of its decision last month to allow imports of Syngenta's biotech sweetcorn Bt 11.
Cleared by Brussels for food and feed - not cultivation - the Council of Ministers had previously failed to reach a qualified majority decision on Bt11.
Critics suggest the Commission move is purely political, linked to pressure from the US - a leading global supporter and supplier of GM food crops - that is pushing Europe to accept GMOs into the food chain. The US charges that its biotech farmers are losing billions of dollars in trade as the borders to Europe remain closed.
"Those countries who rejected today's authorisation are refusing to make life easy for the Commission in its attempts to appease the Bush administration and its business cronies," said Eric Gall at Greenpeace.
If authorised, the maize would be used as any other maize, except for cultivation and food uses. Its authorisation would be for 10 years and it would have to be clearly labelled as being genetically modified. The approval for food uses is pending decision under EU GM Food legislation.
NK603 maize was cleared for crop production in the US in 2000 and in Japan and Canada in 2001, and all these countries allow its use in human food and animal feed. Australia joined the club in 2002 when it cleared the way for NK 603 use in food, although it is still banned in animal feed and crop production.
Non-GM maize, or corn, is grown commercially in over 100 countries, with a combined global harvest of 590 million metric tonnes. The major producers of maize in 2000 were the US, China, Brazil, Mexico, France, and Argentina. Maize is grown primarily for its kernel, which is largely refined into products used in a wide range of food, medical, and industrial goods.