The move comes after clashes with police
Peru's military have been authorised to give support to the police for 30 days in an escalating dispute over Amazon resources with indigenous groups.
The armed forces will intervene to ensure the operation of roads, airports and other essential services, Peru's ministry of defence said.
A day before the protesters said they would begin an insurgency to defend their rights, a threat later withdrawn.
Some 30,000 people have held a month-long protest in Peru's Amazon region.
There have been clashes with the police as the indigenous protesters call for the repeal of decrees passed over the past two years relaxing restrictions over oil exploration and development.
President Alan Garcia has said all Peruvians should benefit from the country's natural resources not just the "small group of people who live there".
"We have to understand when there are resources like oil, gas and timber, they don't belong only to the people who had the fortune to be born there," President Garcia said.
Under Peru's constitution the state is the owner of the country's mineral and hydrocarbon wealth.
On Friday, Alberto Pizango, head of the indigenous Amazonian organisation, AIDESEP, said talks with the government had broken down.
Indigenous leader Alberto Pizango: 'Not against development'
He said their ancestral territories were being handed over to multinational companies without consultation.
But he denied he or the movement of 65 indigenous groups he leads are against development.
"What we want is development from our perspective," Mr Pizango said.
On 8 May the government declared a state of emergency for 60 days in parts of Peru's Amazon region where the protestors have disrupted transportation links including airports and bridges.
Huge stakes are involved, says the BBC's Dan Collyns in Lima. Last month, a French oil company, Perenco, pledged to invest $2bn (£1.32bn) in one rainforest oil field.
Indigenous communities complain that some 70% of Peruvian Amazon territory is now leased for oil and gas exploration, putting at risk their own lives and the biodiversity of the Amazon.
The Peruvian rainforest is the biggest stretch of Amazon outside Brazil.