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In the latest violence, a spokesman for military operations in Papua said 16 civilians were killed and 65 more were wounded in the town of Wamena, where protesters had set buildings ablaze.
Around 20 people died in Indonesia’s West Papua region which has been witnessing an increasing demand for independence.
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Indonesian security forces said Monday that 19 civilians and a soldier had been killed during riots in two towns in Papua.
Protests convulsed the country's easternmost provinces of Papua and West Papua, on the island of New Guinea - collectively known as Papua - for two weeks in late August. The sometimes violent unrest erupted after a group of Papuan students in Surabaya, Indonesia's second city on the island of Java, were taunted and attacked by a mob chanting racial epithets over accusations they had desecrated a national flag.
In the latest violence, a spokesman for military operations in Papua said 16 civilians were killed and 65 more were wounded in the town of Wamena, where protesters had set buildings ablaze.
"For Wamena, based on data on the ground, 16 died and 65 were wounded," spokesman Eko Daryanto said by telephone, adding the situation was now calm.
Papua police said clashes had broken out after a fight between students from different schools in Wamena, the biggest town in the highland interior of Papua province.
"The fight then escalated to burning of government and public facilities as well as private properties," police said in a statement.
Viktor Yeimo, a spokesman for the West Papua National Committee (KNPB), a pro-independence group, said the violence was triggered by racist slurs directed at students by a teacher in the town Saturday. Papuan police said this was not true, following checks with teachers and the school.
President Joko Widodo told reporters that the Wamena violence was triggered by a "hoax", and called on people to screen information posted on social media.
Resource-rich Papua was a Dutch colony that was incorporated into Indonesia after a controversial U.N.-backed referendum in 1969. The region has since endured decades of mostly low-level separatist conflict.
After the August protests began, Indonesia sent about 6,000 additional military and police personnel to the region, and authorities blocked internet access for a time to prevent the use of social media.
Police have rounded up dozens of people for damaging public property in the protests, with several named as treason suspects over a demand for an independence referendum that authorities have ruled out.
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