Indonesian security forces have deployed extra personnel to man the streets of Papuan cities and towns in a bid to control ongoing protests.
Large protests have spread through the Indonesia-ruled Papuan provinces this week in response to racist harassment of Papuans in Javanese cities.
While a protest involving an estimated 20-thousand people in Jayapura on Monday was peaceful, mobilisations in some other centres have turned violent.
Chaos erupted yesterday in Fakfak and Timika, when military forces and police struggled to contain protests that turned into riots.
The government has restricted internet access in Papua in a bid to stem the flow of what it terms "hoax news" which it has linked to the unrest in Papua.
But footage has emerged of protesters in Fakfak being dispersed by security forces firing shots. It's not clear if the shots were fired into the air or aimed at people but at least two Papuans were seriously injured in the melee.
The Guardian reported the police chief in West Papua province, Herry Rudolf Nahak, saying the situation was under control after more than a thousand additional police and soldiers were deployed from other parts of the republic.
More protests are expected in Papua in the coming days, and Indonesian authorities are concerned that anger will spill over again.
Earlier this week in West Papua's capital Manokwari, protesters set fire to the parliament building and blocked roads with burning tires.
In Sorong, over 250 prisoners were able to escape the main jail amid rioting in the town centre.
In Timika, police detained 45 people related to yesterday's riots which caused damage to commercial premises in the town, according to CNN.
Indonesia's Coordinating Minister for Political, Legal and Security Affairs Wiranto, who goes by one name, left Jakarta today for Papua to attend to the security crisis.
He was accompanied by the head of Indonesia's military, Marshal Hadi Tjahjanto, and national police chief General Tito Karnavian.
Mr Karnavian has pointed blame for the unrest in Papua on people who posted on social media about last week's incidents involving Papuan students in Java.
But a spokesperson for the pro-independence West Papua National Committee, Victor Yeimo, said the government was trying to hide the truth by throttling the internet in Papua.
According to him, Papuan university students in cities such as Bogor continue to be subjected to pressure by elements of the local community.
"People from Indonesia come and question them. They have videos, so every treatment by the Indonesian people they record it," Mr Yeimo explained.
"So Indonesia cannot hide the issue. I called the leader of the students dormitory (in Bogor). They said they're now preparing to go back to West Papua."
Meanwhile, the Papua provincial governor Lukas Enembe has voiced concern for the welfare of Papuan students in Javanese cities and has called for those who continue to face harassment to return to Papua.
Along with representatives of the Papuan People's Assembly, Governor Enembe is due to visit Papuan students in Surabaya, Malang and Semarang by tomorrow.
He is also expecetd to talk with Indonesia's president Joko Widodo, who on Tuesday urged Papuans to stay calm and be forgiving.