Indonesian authorities are hunting for more than 250 inmates who escaped from a prison in the province of West Papua.
The prison break happened Monday as protesters took to the streets in several cities blocking roads, and torching buildings including the jail.
The unrest was triggered by the detention of Papuan students in the city of Surabaya over accusations they had disrespected the Indonesian flag.
Police reinforcements have been sent to Papua ahead of more planned protests.
Thousands of Papuans took the streets of cities including Sorong, Manokwari and Jayapura on Monday.
The prison, in Sorong, was set ablaze and rocks were thrown at prisoners, said justice ministry spokeswoman Marlien Lande.
"258 inmates escaped and only five of them had returned by this morning," Ms Lande said, adding that several guards and employees were injured as they tried to stop the escape.
Papua, a former Dutch colony, declared itself independent in 1961 but its larger western neighbour later took control.
A separatist movement continues to this day and Indonesian authorities have faced allegations of human rights abuses in the region.
The latest anger stems from an incident over the weekend involving Papuan students in Surabaya, East Java - Indonesia's second biggest city.
Reports said they disrespected the Indonesian flag in front of a dormitory during celebrations of Independence Day on Saturday.
On Monday police in riot gear fired tear gas and water cannons to disperse the crowds. The protests then spread to other parts of the region on Tuesday.