Protestors in the West Papuan provincial capital of Manokwari have set fire to the local parliament building after a demonstration against the arrest and detention of scores of Papuan students.

A separatist movement has simmered for decades in Indonesia’s easternmost provinces, Papua and West Papua, while Indonesian security forces have been frequently accused of human rights abuses.

The spark for the latest unrest 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 17 August, according to Papuan activists.

Police fired tear gas into dormitories before arresting 43 students, with officers calling the students “monkeys” during the operation, Albert Mungguar, one of the activists said at a news conference on Sunday.

Local media reported Papuan students were forced to barricade themselves in their dormitories, while a vigilante mob threw stones at the building while chanting, “kick out Papuans” and “slaughter Papuans” for hours.

On Monday morning, Papuan protesters set fire to the legislative council building and blocked streets in the provincial capital of West Papua, Manokwari, by burning tyres and tree branches, deputy governor Mohamad Lakotani said.

“The city centre, market, the port are next to the parliament building, as well as shopping centres. 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 told broadcaster TVone that Papuans were angry because of “the extremely racist words by East Java people, the police and military”.

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.

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 criticised UN-backed referendum in 1969.

Exiled West Papuan independence leader Benny Wenda said peaceful protests by West Papuans and supporters across the Indonesian archipelago “have been met with arrests, beatings and abuse given out by the Indonesian colonisers”.

“Every month, the world is given horrifying new evidence of the Indonesian state’s violent intention to crush the West Papuan people’s demand for freedom and self-determination.”

Human rights lawyer Veronica Koman said on Twitter the protests in Jayapura and Manokwari were the largest in years, with demonstrators marching through city streets, some waving the secessionist Morning Star flag.

Last week, the Pacific Islands Forum bloc of countries called on Indonesia to finalise a long-promised visit to the Papuan provinces by the United Nations High Commissioner for Human Rights Michelle Bachelet. The Forum wants a report on alleged human rights abuses within a year.

A spokesman for the Indonesian ministry of foreign affairs said the commissioner’s visit was “on the table” and that negotiations over the visit were ongoing. Indonesia maintains Papua and West Papua are integral and indivisible parts of the Indonesian state, and regards the Free West Papua campaign as an illegitimate separatist movement.

Reuters contributed to this report