Dozens more were injured in the outbreak in protests across Wamena and the West Papuan capital of Jayapura, and Indonesian authorities have rounded up more than 700 people for questioning in the past 48 hours.
Exiled West Papuan independence leader Benny Wenda told SBS News the protests started peacefully and the bloodshed marks a serious deterioration of the situation.
“This is really shocking at a human level, shocking … these students are high school students in Wamena, they are kids,” he said
Mr Wenda spoke to SBS News from New York, where he is attending the UN General Assembly to lobby for the body's High Commissioner for Human Rights to be granted access to his homelands.
“My message to global community is we really need the United Nations peacekeeping force to enter West Papua," he said.
“We are talking about a humanitarian crisis happening [there]."
The independence leader said Australia should support calls for international intervention to investigate the situation.
“I urge the Australian government to quickly act… we don’t want to repeat the same history that is happening in East Timor,” he said.
Riots broke out in Wamena and Jayapura after Indonesian forces confronted hundreds of protesting high-school students.
The mob of Papuans had torched local government buildings, shops and homes during riots in the highlands town of Wamena.
The fresh protests were triggered by allegations a teacher racially abused a student.
In Jayapura, video of protests appeared to show gunshots and tear gas being fired as clashes with demonstrators descended into chaos.
Indonesian President Joko Widodo has called for calm to defuse unrest in West Papua but has since urged residents “not to be provoked” into protests by hoaxes.
Prime Minister Scott Morrison deferred question over the surge in violence to Foreign Minister Marise Payne, who urged “absolute restraint” to deescalate the situation.
“We are obviously very concerned about the reports of violence in Papua [and] West Papua,” she said.
“They are matters which our post in Jakarta is following up with authorities there.”
The death toll of the latest violence is thought to have risen after a dozen more bodies were found under the burnout wreckage of buildings.
But Indonesia analyst and Professor of International Politics at Deakin University Damien Kingsbury told SBS News evidence depicted numerous people have been injured with gunshot wounds.
“There is clear evidence that the Indonesian security forces have used live ammunition, there is extensive recordings of the gunfire itself and automatic weapons fire,” he said.
“The Indonesian claims that there were shooting from both sides seems to be unfounded."
Activists have identified some of those allegedly shot dead in Wamena and Jayapura as 26-year-old Ketron Kogoya, 23-year-old Yery Murib, and 17-year-old Hermanus Wesareak.
Internet access was initially cut off when the protests took hold – but has since been restored to Jayapura.
Indonesia’s control of the territory has long been a flashpoint of tensions among Indigenous locals with low-level conflict and such movements simmering for decades.
But Camellia Webb-Gannon, coordinator of the West Papua Project at the University of Wollongong, said social media has helped shed light on recent unrest gripping West Papua.
“What has changed is the presence of social media and increased international networks,” he said.
“The world is finding out more about West Papua and what’s going on there.
“Indonesia has had a media ban in the province for decades.”
Authorities claimed most victims of this recent outbreak in violence were non-Papuans, blaming the unrest on Papuan separatist movements.
Indonesian National Police chief Tito Karnavian told a news conference in the capital Jakarta, the situation had calmed after more police and soldiers being deployed to the region.
“It was planned by a certain group in time for the UN general assembly. In Wamena there was a plan by the separatist movement to set up a hoax,” he said.
An Indonesian soldier was among three people killed in Jayapura, where security forces and stone-throwing protesters clashed on Monday.
The soldier is believed to have been stabbed to death and three students died from rubber bullet wounds, authorities said.
Thousands are thought to have fled to shelters following the outburst of bloodshed that saw civilians burned alive in buildings set ablaze by protesters.
Authorities confirmed more than 4,000 including mothers and their children, fled to military and police posts, government buildings and a local church to seek shelter.
Mr Kingsbury said Australia has long been reluctant to speak out on matters relating West Papua's political turmoil, even before it signed a treaty recognising Indonesia’s sovereignty of the region.
“Australia’s reluctance to become involved in West Papua … really is a reflection of [its] sensitivity towards Indonesia and a desire to not seen to be interfering in matters concerning Indonesian sovereignty,” he said.