A separatist movement has simmered for decades in Papua, while there have also been frequent complaints of rights abuses by Indonesian security forces.
The spark for the latest anger appears to have been the detention of scores of Papuan students in Surabaya, East Java, for bending a flagpole in front of a dormitory during the celebration of Indonesia's Independence Day on Aug. 17, according to Papuan activists.
Police fired tear gas into the dormitory before arresting 43, with officers calling the students "monkeys" during the operation, Albert Mungguar, one of the activists said at a news conference on Sunday.
On Monday morning, Papuan protesters set fire to a local parliament building and blocked streets in the provincial capital of West Papua, Manokwari, by burning tires and tree branches, Deputy Governor Mohamad Lakotani said.
"The city center, market, the port are next to the parliament building, as well as shopping centers. Everything's affected. Practically, the whole city is not running, if not to say completely paralysed," Lakotani told Kompas TV.
Television footage showed a group of about 150 people marching on the streets in Manokwari, as well as footage of smoke billowing from a parliament building.
Papua Governor Lukas Enembe said Papuans were angry because of "the extremely racist words by East Java people, the police and military", he told broadcaster TVone.
National police spokesman Dedi Prasetyo said security personnel were trying to calm the situation.
"Negotiations and communication are ongoing. Generally the situation is under control," Prasetyo, who is based in Jakarta, said by text message.
A separate, peaceful protest of about 500 people was also underway in the town of Jayapura, the capital of Papua province, Papua police spokesman Ahmad Kamal said by phone.
The Papua and West Papua provinces, the resource-rich western part of the New Guinea island, makes up a former Dutch colony that was incorporated into Indonesia after a widely criticized U.N.-backed referendum in 1969.
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