Indonesian police have defended their decision to storm into a dormitory of West Papuan students alongside the nation's military, over vigilante allegations that someone had committed slander on the national symbol.

Key points: Police arrested 43 students but released them without charge over allegations of "committing slander on the national flag"

Police arrested 43 students but released them without charge over allegations of "committing slander on the national flag" Earlier this week pro-West Papuan protesters were attacked and hundreds arrested

Earlier this week pro-West Papuan protesters were attacked and hundreds arrested The acquisition of West Papua by Indonesia has long been a cause of controversy

Police and armed military personnel stormed through the gates of the dormitory in the Indonesian city of Surabaya, firing around 20 tear gas canisters into the building, causing injuries, last Saturday.

Forty three students were arrested and taken to a police station in the city, but released around nine hours after without charge, over claims that the Indonesian flag was found in the gutter by the building.

Indonesian President Joko Widodo has sought to ease tensions, with his Chief Security Minister pledging a "complete and fair" investigation into the incidents.

Mr Widodo called for calm in Papua and urged people not to damage public facilities.

"It's OK to be emotional, but it's better to be forgiving," he said.

"Patience is also better."

Today, protesters torched a local parliament building and set fire to tyres and branches in the West Papua provincial capital, Manokwari.

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A separate, peaceful protest of about 500 people was also underway in the town of Jayapura, the capital of Papua province.

The protests appears to be in retaliation to the detention and treatment of West Papuan students in Surabaya between Friday night and Saturday afternoon.

Nationalist vigilantes gathered outside the student's dormitory building from Friday night — a day before Indonesia's independence day —singing the Indonesian national anthem, cutting power to the building, and attacking good Samaritans delivering food and drinks to the trapped students.

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The mob grew the following day, with videos of the scene catching chants of "get rid of the Papuans right now" and "monkeys, get out".

East Java police spokesperson Frans Barung, told the ABC the police and military stormed in as a response to concerns that the crowd "was close to attacking".

"[We entered] due to the [students'] provocative actions on allegedly committing slander on the national flag … the police simply acted as a stabilator," he told the ABC.

Human rights lawyer Veronica Koman told the ABC five people were injured during the incident.

"Racist Indonesian ultra-nationalists insist that West Papuans can't be free, but they don't want West Papuans at the same time too," she said.

A separatist movement has simmered for decades in Papua, while there have also been frequent complaints of rights abuses by Indonesian security forces.

Papua Governor Lukas Enembe said Papuans were angry because of "the extremely racist words by East Java people, the police and military", he told Indonesian broadcaster TVone.

Indonesia's 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," Brigadier General Prasetyo, who is based in Jakarta, said by text message.

Hundreds of protesters attacked and arrested

Flare-ups such as these are considered common around August 17, which marks the Indonesian proclamation of independence and freedom from Dutch colonial rule in 1945.

West Papua and Papua, often referred to collectively as West Papua, are the easternmost provinces of Indonesia and their acquisition has been the cause of controversy for more than 60 years.

43 were arrested from the dormitory building after police stormed in. ( Supplied: Victoria Koman )

In a separate incident on Friday, demonstrators protesting the anniversary of the 1962 New York Agreement, which paved the way for Indonesian control of West Papua, were also forcibly dispersed and attacked by civil militia under police watch, Ms Koman said.

More than 100 protesters were arrested that day and Ms Koman said they were beaten, verbally abused, kicked and had rocks thrown at them because police "failed to intervene".

"The incident shows a worsening trend of repressive tactics against West Papuans and Indonesians speaking about West Papua issue," Ms Koman said.

A man was injured by tear gas being shot inside the dormitory building. ( Supplied: Veronica Koman )

"Peaceful protesters were attacked by civil militias under the police's watch, but then they are often framed in [domestic] media as the rioters."

The city of Malang's deputy mayor, Sofan Edi Jarwoko, said students from the embattled region should be forcibly removed due to unrest following the incident, according to reports by local media.

At the Pacific Islands Forum in Tuvalu, regional prime ministers and presidents also discussed concerns about human rights abuses by the Indonesian Government in West Papua, urging a strong call for Jakarta to take action.

The Indonesian provinces of West Papua and Papua, are often referred to collectively as West Papua. ( ABC News: Jarrod Fankhauser )

ABC/Reuters