At a regulatory committee meeting on the release of genetically modified organisms into the environment, the group rejected proposals from the EU's legislative body, the European Commission, that called for five European countries - Austria, France, Germany, Greece and Luxembourg - to repeal their bans on specific GMOs within 20 days.
The bans, introduced between 1997 and 2000, focus on three maize and two rapeseed types approved before the EU began its unofficial biotech ban in 1998 that ended earlier this year.
Each of the Commission's proposals, failed to get the required qualified majority of 232 votes out of 321, with some, such as Bt-176 maize made by Swiss biotech giant Syngenta showing more opposition, than support. A considerable 221 votes went against lifting the Bt-176 maize ban, compared to 54 votes for and 46 abstaining.
The Commission proposals will now go to a Council of Ministers meeting in the new year.
Environmental groups welcomed the outcome.
"The European Commission only survived today by a handful of votes. European countries should be congratulated for not supporting these outrageous proposals," said Friends of the Earth Europe's GM campaigner Adrian Bebb.
Despite tough new European rules to track and label genetically modified organisms enforced in April, food makers are opting to skip GM ingredients in European food formulations because they know the suspicious European consumer will refuse to buy GM food products.
Critics of the Commission believe it is caving into pressure from the US that last year filed a case against the EU at the World Trade Organisation claiming that Europe's precautionary stance on GM food, including the national bans, is a barrier to free trade and harms their farmers.
At the same meeting the environmental experts failed, again, to come up with a majority decision to allow US biotech firm Monsanto's genetically modified maize MON 863 for import and processing into the EU.
The meeting yesterday was a further attempt by the European Commission to push through approval for the MON 863, cleared earlier this year on risk assessment by the European Food Safety Authority (EFSA) but two months ago member states failed to give it the green light.
After the failed vote yesterday, the decision now passes to the Council of Ministers. If no decision is taken after three months, as observers believe to be likely, the Commission can adopt it under legal loophole.
Facing the fury of anti-GM campaigners, in May this year the Commission used this legal capacity to approve a GM sweetcorn supplied by Swiss biotech firm Syngenta to enter the food chain - the first approval of a GM foodstuff since 1998 and marking the end of the de facto moratorium set up in 1998. MON810, a biotech maize engineered by Monsanto to be resistant to the European corn borer, became the second approval since the ban when cleared within months of Syngenta's product.
MON 863 will become the third, if given the green light next year.