BRUSSELS, April 15 (Reuters) - Austria and Luxembourg will be allowed for now to keep their controversial bans on a gene-altered type of maize, despite a European Commission ruling that the bans were unjustified, the Commission said on Wednesday.

The 15-nation European Union approved the use of the maize, produced by Swiss agrochemical multinational Novartis, in December 1996 following a request from France, a major cereals producer.

Vienna and Luxembourg, which had voted against the proposal, subsequently slapped domestic bans on the maize on the grounds that it could pose a risk to health and the environment.

Novartis maize is genetically engineered to resist the herbicide glufosinate and contains a so-called Bt toxin designed to ward off the corn- borer pest.

Austria, Luxembourg, Greece and environmental groups like Greenpeace have said they fear the maize could pass on its herbicide resistance to other plants while the Bt-gene could also kill benign insects relied on by organic farmers.

The Commission -- the EU's executive arm -- ruled last September there was no scientific basis for this claim and said the bans should be repealed because they broke the bloc's internal trade rules.

But the Commission's proposal failed on Monday to win the support of a sufficient number of EU governments, Commission spokesman Peter Jorgensen told reporters on Wednesday.

Scientific advisers from Austria, Luxembourg and Greece opposed the Commission plan, while their French, Belgian, Danish and Irish colleagues abstained, an EU source told Reuters.

"We abstained because we wanted to show we understood the sensitivity of the issue in certain member states," a French diplomat explained.

"We didn't want to vote against the Commission because they are right but we didn't want to clash with public sensitivities in Austria or Luxembourg either. It's not up to us to point a finger at others. That's the Commission's job."

Under the EU's convoluted rules, the issue will now be put to the bloc's environment ministers, who next meet on June 16.

If at that meeting the Commission again fails to win sufficient endorsement for its proposal, it will find itself in the awkward position of having to take Austria and Luxembourg to the European Court of Justice in Luxembourg for breach of EU trade rules, knowing it does so without the backing of the governments on whose behalf it acts.

The Commission has made no secret of its exasperation at the bloc's arcane procedures and has proposed a reform of the rules.

One source close to the discussions said this was not the first time France appeared to have changed its mind after seeking EU authorization for a genetically-altered crop.

Paris sought and received EU approval to import, grow and market a gene- changed rapeseed but announced last November it had decided not to give the crop the green light after all.

"Later research showed the modified gene in this type of crop could be transmitted to other plants," a French diplomat explained. She said the risk of transmission did not exist in the case of genetically-engineered maize and soybean.

EU states are due on Friday to approve four new varieties of gene-altered maize and rapeseed.

Jorgensen said the strains had been developed to give them similar resistance characteristics to the Novartis maize and the gene-changed soybean sold by U.S. agrochemical giant Monsanto, whose approval by the EU a year ago sparked off so much uproar.