Children are at far greater risk than adults from poisoning by mercury, a potent neurotoxin that can cause brain and central nervous system damage.
"They are 10 times more sensitive to the effects of mercury," Fernandez said in a phone interview after presenting the findings to Peru's Environment Ministry.
The study by the Stanford, California-based institution examined a rainforest region of great biodiversity that includes natives living in voluntary isolation and where Peru's government has struggled in vain to control informal mining.
Researchers sampled hair from 1,029 people in 24 communities beginning last year. A quarter of the subjects work in the region's wildcat alluvial gold mining industry, where an estimated 35 metric tons a year of mercury is used to bind together gold flecks. The mercury is then burned off and enters the environment.
Fernandez said the explanation for greater mercury contamination among indigenous populations is their consumption of fish. His group's study of fish in the region found 60 percent of species contained unacceptable levels of mercury.
Peruvian authorities recently extended until August 2014 a deadline that was to have expired this month for the estimated 40,000 miners in the region to formalize their claims or leave.
Official efforts until now to halt illegal mining have been stymied by violent protests.
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Associated Press writer Frank Bajak contributed to this report.