However, protesters told Reuters that police had opened fire on them from helicopters.
Rights group Amazon Watch on Monday condemned what it described as a "violent raid" by police, saying witness reports indicated the unarmed demonstrators were attacked by police while sleeping alongside a road.
It also said some wrestled guns off police officers and fought back "in self defence".
The toll is expected to climb in the latest incident, thought to be the most violent so far, as dozens of people were reported injured.
"I hold the government of [Peruvian] President Alan Garcia responsible for ordering the genocide," indigenous leader Alberto Pizango told journalists in Peru's capital, Lima, on Friday.
Demonstrations erupted in Peru's native communities in response to government moves to open the region to oil exploration and development by foreign companies under a set of measures that Garcia signed in 2007 and 2008.
The government on May 8 declared a 60-day state of emergency in areas of the Amazon, suspending constitutional guarantees in an attempt to suppress the protests, which have targeted airports, bridges and river traffic.
Protesters from a movement of 65 indigenous groups had declared an "insurgency" against the government for refusing to repeal the laws that threaten their ancestral land and resources. They later withdrew their decision.
The indigenous groups were backed by the International Federation of Human Rights, which groups 155 human rights organisations from around the world.
It called on Peru to rescind the decrees because of the government's failure to consult indigenous peoples.
Government officials acknowledge that the country's indigenous groups have historically been marginalised, but insist that Peru's constitution makes the state the owner of the country's mineral wealth.