At a council meeting this week the ministers were unable to reach a majority decision on a Commission proposal to approve the importation and feed use of Monsanto's GT73 GM oilseed rape into the EU.
The European Commission asked ministers to take a decision after member state experts failed to reach an agreement in June.
The major food use of rape, also known as canola, in North America and Europe is as a refined vegetable oil. Typically, rapeseed oil is used by itself as a salad oil or cooking oil, or blended with other vegetable oils in the manufacture of margarine, shortenings, cooking and salad oils.
But with the 25 member state ministers failing to reach a qualified majority this week to allow Monsanto's oilseed rape - designed to resist the company's chemical herbicide - into the EU, the decision is now shunted onto the Commission.
Under an obscure facet of the law known as the 'comitology procedure', Brussels could actually push the GT73 food crop, already cleared a risk assessment by the European Food Safety Authority (EFSA), through to law because the council has failed to reach a majority decision. Observers believe the Commission may opt to take this path.
Facing the fury of anti-GM campaigners, earlier this year the Commission broke the de facto moratorium on GM foods and pushed through approval for a GM sweetcorn supplied by Swiss biotech firm Syngenta to enter the food chain. The first approval of a GM foodstuff since 1998.
Although the member states had failed to give the green light for the GM corn, the Commission pushed it through under the comitology procedure.
Environment group Friends of the Earth Europe urged the Commission this week to follow the majority of European environment ministers.
Geert Ritsema, GM coordinator for the group said: "The new EU Commission must listen to the opinion of the 19 environment ministers who voted against the introduction of this genetically modified oilseed rape. There is clearly a big difference in opinion between the member states, the Commission and its food safety authority."
But the biotech industry was disappointed by the outcome this week claiming that EU members members states are "ignoring" the very laws on GM crops that they and the European Parliament have set up over the past five years.
"Member states are not facing up to their responsibilities," commented Simon Barber, director of the plant biotechnology unit at EuropaBio, the European association for bioindustries.
Brussels recently pushed through tough new rules on the labelling of GM ingredients in a bid to make such foodstuffs more easily accessible to the market.
But GM ingredients are regarded with some suspicion by consumers in Europe and as such are used infrequently in food formulations by food manufacturers who do not want to see sales dip.