The United States called on Indonesia to ensure due process and address grievances in the restive Papua region after a court indicted five activists for treason.

The court in Indonesia, a nation which has warming relations with the United States, prosecuted the men after they raised an outlawed Papuan flag and declared independence at a peaceful gathering. They face life in prison if convicted.

"We urge the Indonesian authorities to ensure due process and procedural safeguards in accordance with Indonesian law and Indonesia's international legal obligations for all persons indicted," a State Department spokesperson said, speaking on condition of anonymity.

"We encourage the Indonesian government to work with the indigenous Papuan population to address their grievances, resolve conflicts peacefully and support development in the Papuan provinces," the spokesperson said.

The United States "recognizes and respects the territorial integrity of Indonesia within its current borders, which include the provinces of Papua and West Papua," the spokesperson stressed.

Jakarta in 1969 took control of Papua, a former Dutch colony on the western half of New Guinea island whose people are ethnically distinct from most Indonesians.

The region has since seen a low-intensity insurgency. Foreign journalists are barred from reporting in the region.

Local television footage in October showed the five men declaring independence in the Papuan capital Jayapura and paramilitary police then shooting into the crowd and beating participants with batons and bare fists.

At least three people were killed and more than 90 injured. Eight police officers were let off with written warnings for disciplinary infractions.

President Barack Obama's administration has sought greater ties with Indonesia, pointing to its rapid transition to democracy and moderate brand of Islam.

In 2010, the United States said it would resume ties with Indonesia's elite Kopassus unit after a 12-year hiatus due to human rights concerns.