The findings in the Sierra Norte de Oaxaca region will stoke the row about whether it is possible to control GM crops and their potential threat to genetic diversity.

The group of researchers from the University of California, Berkeley, detected the contamination in October last year while working with a biological laboratory in the region. They compared indigenous corn with samples known to be free from genetic engineering, as well as with genetically modified varieties.

Their results, published yesterday in the science journal Nature, showed that four of six samples of native criollo corn taken from fields contained a genetic "switch" commonly used in GM crops, and that two of the samples were found to have another DNA segment commonly inserted by genetic engineers. A further sample contained a commonly inserted gene that prompts the plant to produce a poison.

The researchers alerted the Mexican government which did its own tests in 22 communities. They confirmed in September this year that transgenic DNA had been found in 13 of them, with contamination of between 3% and 10%.

The results are surprising because Mexico, which is the genetic home of maize, has banned the growing of GM maize since 1998, and the last known GM crops grown in the region were almost 60 miles from where the contaminated maize was found.

It was not clear yesterday when the contamination took place, but the scientists speculated that it originated from GM maize bought from the US as food aid for the impoverished region in central Mexico, and had progressed over time via multiple pollinations.

It is not thought that that the cross-pollination happened over long distances, because corn pollen is heavy and does not travel far on the wind.

"I repeated the tests at least three times to make sure I wasn't getting false-positives," the lead author of the report, David Quist, said. "It was initially hard to believe that corn in such a remote region would have tested positive."

"This is very serious," said Ignacio Chapela, assistant professor of microbial ecology at Berkeley's College of Natural Resources, "because the regions where our samples were taken are known for their diverse varieties of native corn, which is something that absolutely needs to be protected. We can't afford to lose that resource."

But Luis Solleiro, director of the Mexican biotechnology trade association, denied that the country's rich genetic diversity was threatened. "The data suggests that any transgenic corn is at a very low level," he said. "This level, or even greater presence, would not adversely affect the genetic diversity of native strains."

Greenpeace, Friends of the Earth and other groups that oppose GM crops argued yesterday that even a low level of genetic contamination was highly significant in a centre of diversity and origin.

"The genetic contamination is likely to multiply through pollen flow and spread further to other traditional varieties and wild relatives growing in the area", Doreen Stabinsky, from Greenpeace USA, said.

"This is likely to be only the tip of the iceberg, as plants in other parts of Mexico have not yet been investigated."

The UN Food and Agriculture Organisation is concerned that GM crops may pollute the gene pool of conventional relatives in the same area or nearby, depending on wind and insects. "If there is no barrier to pollination, you get this potential hazard," said Ricardo Labrada Romero, the FAO's plant protection officer.

The research adds to concerns that GM crops may be out of control. The Canadian government's agricultural de partment last month reported that stray pollen and seed from genetically modified oilseed rape crops was now so widespread that it was difficult to grow conventional or organic strains without them being contaminated.

More than 100m acres [33m hectares] of GM crops have been grown, mostly in the US and Canada.