Up to 50 armed gunmen attacked the Pirime Police Station near Wamena, an isolated highland town with a population of around 10,000.
The gunmen set fire to the station before fleeing with several police weapons into the surrounding forests. The bodies of the police officers were found in the remains of the station.
Around 100 special Mobile Brigade officers have been sent to Pirime to help with investigations, a report in The Jakarta Post newspaper said.
"The shootings by unknown assailants took place at 4 a.m. this morning in Pirime, about eight hours drive from Jayapura, Papua's provincial capital," National Police Chief Gen. Timur Pradopo said.
The Post report said Timur refused link the gunmen to the separatist Free Papua Movement.
"My officers are still investigating the incident, let's wait," he said.
The provinces of West Papua and Papua together are about the size of Spain and occupy the western half of the island of Papua. Papua New Guinea occupies the eastern half.
The attack is the latest in the sensitive region with a history of low-key but often brutal violence by independence movements and comes ahead of this weekend's local celebrations of Free Papua Movement.
Two policemen were killed in Puncak Jaya highland in a remote area of Papua province, around the time of annual Free Papua Movement celebrations a year ago.
Rebel independence groups claim rural poor are being exploited by big international forestry and mining corporations.
Papuans are ethnically Melanesian and closer to Australia's aborigines than the Asians who make up most of Indonesia's population. Papuans also say their culture and identity is being eroded by an influx of Asian Indonesians.
West Papua and Papua provinces have been a part of the Indonesian archipelago federation since the Dutch gave up their colonial rule and a slim majority in a controversial referendum in 1969 voted in favor of joining.
Since then various separatist movements have been pushing for independence and relations between the population and security forces have remained uneasy.
In June Radio Australia reported three Papuan civilians and two soldiers were killed around Wamena when violence erupted over a road accident.
Local media reports said the violence began when two Indonesian soldiers on a motorcycle hit and killed a small boy.
Villagers allegedly retaliated and killed the two soldiers.
Indonesian police and military then responded violently and later burned down houses, the Radio Australia report said. An Indonesian military spokesman denied the army destroyed houses.