Campaigners say the men had received several death threats from illegal loggers, who are suspected of being behind the killings.
Correspondents say indigenous people have felt under increasing threat from deforestation in recent years.
The men included the outspoken anti-logging activist Edwin Chota.
Mr Chota and three others were killed near Saweto on the border with Brazil, Peruvian officials said.
Officials said that they are believed to have been killed over a week ago as they attempted to travel to a meeting in Brazil.
A 2012 World Bank report estimates that 80% of Peruvian timber export stems from illegal logging.
Under threat Professor David Salisbury from the University of Richmond knew Mr Chota for several years, and said that he was targeted because he "threatened to upset the status quo".
"The illegal loggers are on record for wanting Edwin dead," he told the Associated Press.
Mr Chota had campaigned against illegal logging for at least six years and written hundreds of letters to officials on the topic.
The BBC's Wyre Davies says indigenous peoples such as the Ashaninka have seen their numbers dwindle and their lands come under threat from development.
Recent footage of previously uncontacted Amazon tribes wandering into settled areas has raised fears that they are being forced out of their lands.
Source from: BBC news 09th Sep 2014