Demonstrations erupted in response to government moves to open the region to oil exploration and development by foreign companies under a set of measures that Alan Garcia, the Peruvian president, signed in 2007 and 2008.
French oil company Perenco last month announced plans to invest more than $2bn to develop a field in the Maranon River basin in northeastern Peru.
Alberto Pizango, the leader of the Peruvian Jungle Inter-Ethnic Development Association (Aidesep) said agreed "to declare our peoples in insurgency against the government of President Alan Garcia in the indigenous Amazon territories".
"This means our ancestral laws will become obligatory laws, and we will regard as aggression any force that tries to enter our territory," he said.
His statement followed the government's May 8 declaration of a 60-day state of emergency in areas of the Amazon, suspending constitutional guarantees in an attempt to suppress protests, which have targeted airports, bridges and river traffic.
Talks between protest leaders and Yehude Simon, the cabinet chief, in Lima on Wednesday failed to defuse the conflict.
The decrees eased restrictions on oil and other forms development in territories claimed by indigenous groups.
|Pizango said the indigenous groups wanted development from their perspective [EPA]
"This is not a mere whim. The government has not consulted us.
"We are not against development even though we are portrayed as being against the system. What we want is development from our perspective," Pizango said.
"The government wants to take our territory to give it to the big multinational companies.
"There are riches there like oil, wood, gold - riches that arouse the ambitions of the world's wealthy," he said.
The indigenous groups on Tuesday gained the backing of 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.
Antonio Brack, the environment minister, told reporters on Tuesday: "Undersoil resources do not belong to the indigenous people but to all Peruvians."