Transcript
Unrest was triggered when dozens of Papuan university students in Surabaya were assaulted by a mob on Saturday and later arrested.
One of the students had allegedly trashed an Indonesian national flag on the country's independence day anniversary
These angry scenes were echoed in an incident in the city of Semarang when a Papuan student dormitory was surrounded by civilian groups demanding the students fly the Indonesian flag.
Nationalist sentiment was running high at the weekend, as it always does on independence day.
A researcher with Human Rights Watch, Andreas Harsono, says anti-Papuan sentiment is on the rise in Indonesia.
"Military-related militias are starting to increase their campaign against Papua by showing that the Papuans (are) refusing to raise the Indonesian flag, hoping that it will exasperate the situation on the island of Java, Indonesia's most important island."
The students were called "monkeys" and other racist slurs, sparking thousands to march in the streets back in Papua.
In Manokwari, videos posted to social media showed the parliament building on fire and roads blocked by burning tires.
Indonesia's president Joko Widodo made an appeal to Papuans.
"I know that there are hurt feelings, but as fellow citizens the best thing is to forgive each other. It is ok to be emotional, but forgiving is better. Being patient is also better. And be confident that the government will continue to safeguard your dignity and prosperity."
Indonesia's police chief Tito Karnavian has focussed blame for the destruction in Manokwari on the people who posted about the Surbaya incident on social media, describing it as hoax news.
But US-based Papuan independence leader Octo Mote says this response, along with that of the president's, is disappointing.
"Now the Indonesian president, he ignored what's going on. The he said, 'ok guys just apologise to each other'. So West Papuans should apologise for what? He doesn't condemn the racism. He doesn't say racism is not right."
According to Mr Mote, harassment of Papuans seen in Javanese cities is a long running problem.
He says the allegation about Papuans disrespecting the Indonesian flag in Surabaya was simply used as a trigger by the mob who laid siege to the students' dorm.
"Because of that hatred, they try to find a way. That's what happens not only there, but that same incident happens in so many cities outside of Papua. as a journalist who worked there so many years, we experienced this in our daily lives under Indonesian colonialism the discrimination and racism, we experience in everyday life."
The protests resulting from the outrage over the Surabaya incident have been the biggest in years.
There have been surprisingly few arrests, even where the protests turned violent such as in Manokwari.
On Tuesday a local resident, Lucu Sawaki, said the city's streets had quickly returned to normal calm.
"Police is still everywhere and the security is also good this morning but still people are still afraid to go out from the house, so just couples, motorcycles and cars but it's not like in the past."
But the monkey slurs directed at Papuans in Indonesia's cities have provided a new impetus for Papuan protest.
Yesterday, large mobilisations took place in other Papuan cities, including Merauke, Biak and Nabire.
However in Sorong, as Papuans took to the streets, 250 prisoners escaped from the local jail, amid the chaos.
But in signs of an impending crackdown, Indonesia has deployed more military forces to Papua to quell the unrest.
This is Johnny Blades.
