By JAMES KANTERBRUSSELS — Madeira is more than 500 kilometers from the African coast and is officially one of the “outermost regions” of the European Union.

Despite that far-flung status, Madeira catapulted into the center of the Union’s agricultural and environmental affairs last year when Portugal asked the European Commission for permission to impose an unprecedented ban on growing biotech crops there.

Last week, the commission quietly let the deadline pass for opposing Portugal’s request, allowing Madeira, which is one of Portugal’s autonomous regions, to become the first E.U. territory to get formal permission from Brussels to remain entirely free of genetically modified organisms.

Madeira now will probably go ahead and implement the ban, a spokeswoman for the Portuguese government said Friday.

Individual European countries and regions have banned certain genetically modified crops before. Many consumers and farmers in countries like Austria, France and Italy regard the crops as potentially dangerous and likely to contaminate organically produced food.

But the case of Madeira represents a significant landmark, because it is the first time the commission, which runs the day-to-day affairs of the European Union, has permitted a country to impose such a sweeping and definitive rejection of the technology.

The Madeirans’ main concerns focused on preserving the archipelago’s biodiversity and its forest of subtropical laurel trees.

Such forests, known as laurisilva, were once widespread on the European mainland but were wiped out thousands of years ago during an earlier period of climate change.

That has left Madeira with “much the largest extent of laurel forest surviving in the world, with a unique suite of plants and animals,” according to the United Nations Educational, Scientific and Cultural Organization, which named the Madeiran laurisilva a World Heritage Site in 1999.

The forest also is a growing attraction for tourists, who make up a significant portion of Madeira’s earnings.

In seeking to ban biotechnology on Madeira, the Portuguese government told the commission that it would be impossible to separate crops containing genetically engineered material from other plant life.

The “risk to nature presented by the deliberate release of GMOs is so dangerous and poses such a threat to the environmental and ecological health of Madeira, that it is not worthwhile risking their use, either directly in the agricultural sector or even on an experimental basis,” the Portuguese told the commission, using the acronym for genetically modified organisms.

In an internal memorandum seen by the International Herald Tribune, the commission said it had let the deadline in the Madeira case pass without a formal assessment and more fanfare because that could “create misunderstandings and send confusing signals” at a time when Europe was reconsidering its approach to cultivating GMOs.

In reality, the Madeira case marks the unofficial beginning of a new — and potentially highly contentious — policy that would give European nations and regions far greater freedom to decide when to ban such crops.

In return for that freedom, skeptical countries like Austria would be expected to drop their opposition at E.U. meetings to approving more biotech crops for cultivation, allowing countries and regions that do wanted to plant them to do so.

The policy would be aimed at overcoming an institutionalized stalemate in Europe that has left governments unable to reach decisions on whether to allow cultivation of new biotech products.

As a result of that stalemate, only two biotech crops are allowed in Europe: a corn called Mon 810 from Monsanto and a potato called Amflora from the German industrial group BASF.

John Dalli, the E.U. commissioner for health and consumer affairs, is expected to present details of the new policy by summer, and he will almost certainly have the full backing of José Manuel Barroso, the president of the commission, who suggested the policy last year.

Even so, the new policy is unlikely to be without its problems.

A key concern is a sudden proliferation of bans dotting the continent. That could make it impossible for farmers to grow such crops over any significant amount of territory.

The policy also risks stirring up new questions about whether the bloc is condoning impediments to trade with key partners like the United States.

U.S. agricultural companies like Monsanto have long complained about lack of access to European markets and, in particular, about restrictions on cultivating crops.

In one of the most contentious recent cases in trans-Atlantic trade policy, the World Trade Organization ruled against European restrictions on imports and cultivation of genetically modified crops in 2006.

Mr. Dalli said in a recent interview that concerns about renewed trade tensions with the United States over GMOs were greatly exaggerated.

Mr. Dalli also said that his priority was to get experts, companies and activists to “understand and accept a process that they will not try to second-guess or try to attack once a decision not to their liking is taken.”

That may yet prove to be a tall order at a time when such profound differences of opinion over the potential damage that biotech crops could unleash show few signs of diminishing.

The commission’s decision to allow Madeira its ban came only four months after the European Food Safety Authority, the main body tasked with advising the commission on food safety, categorically recommended ignoring Portugal’s concerns about the effect of GMOs.

The agency concluded in January that, “no new scientific evidence, in terms of risk to human and animal health and the environment, was provided that would justify a prohibition of the cultivation of GM plants in the Autonomous Region of Madeira.”