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In the eastern part of the archipelago, armed conflicts and a pro-independence movement has been going on for decades, with frequent complaints of rights abuses by Indonesian security forces.
Protests in the Indonesian provinces of Papua and West Papua called for independence Monday, following two days of mobilizations against the harassment and arrest of students in Surabaya city over the weekend.
The protests were organized after the arrest of 43 college students, whose dormitories in the city of Surabaya in Java were surrounded by Indonesian nationalists on Friday and Saturday for allegedly disrespecting the country's flag.
Police fired tear gas into the dormitory before arresting 43 students, Albert Mungguar, an activist, said in a news conference on Sunday, adding that the students, who were released the same day without charges, were called "monkeys" during the operation.
The Deputy Governor of West Papua, Mohamad Lakotani, who met protesters in Manokwari, said Papuans demanded an apology for the slur against the students, as well as protection for anyone studying across the archipelago.
"We apologize because this does not represent the voice of the people of East Java," the province's governor, Khofifah Indar Parawansa, said in a televised statement and called the slur "someone's personal outburst of emotion".
Large crowds also took to the streets of Jayapura, the capital of Papua province, though the protest appeared peaceful in television images.
Thousands of Papuans protested in the cities of Manokwari and Sorong, blocking streets by burning tires and tree branches.
Papuans were angry because of "the extremely racist words used by East Java people, the police and military," Papua Governor Lukas Enembe told broadcaster TVone.
"Instead of investigating the racist military personnel who could be seen in video shouting 'hey monkeys, get out', or police who disproportionately fired shots into West Papuans' dorm, police decided to go after who caused the viral content," said human rights lawyer Veronica Koman on Twitter.
The Indonesian government restricts internet access in West Papua to “limit hoax”.
I have not seen any hoaxes today. Today’s protests are the largest people power protests in years
This measure violates freedom of expression and right to access information of West Papuan people
In Manokwari, the capital of West Papua province, protesters set fire to parliament and office buildings, pulled down power poles and burnt vehicles, Lakotani said by telephone.
While in Papua's capital, Jayapura, thousands drove through the city on motorcycles demanding the independence of the two provinces.
According to Amnesty International, Indonesian security forces have killed 95 people, 85 of them indigenous, between 2010 and 2018 at pro-independence political events and social protests in the two restive Papuan provinces, without any of the cases being taken to civil courts.
Papua and West Papua provinces, the resource-rich western part of the island of New Guinea, were a former Dutch colony that was incorporated into Indonesia after a widely criticized U.N.-backed referendum in 1969.