Mobs stabbed an onlooker to death, injured four other people and burned five shops, four cars and more than 20 motorbikes on Thursday, hours after they learned police had shot and killed Mako Tabuni, the deputy chairman of the National Committee for West Papua.
Shops were closed Friday, and many people were afraid to leave their homes.
“It is safe and quiet now. There are many troops on the streets,” said Papua police chief Major General Bigman Lumban Tobing.
He said police detained three people and seized several handmade bombs, machetes, arrows, separatist flags and documents during a raid in a student dormitory in Jayapura.
A low-level insurgency in the province remains an extremely sensitive issue for the government, which restricts access to foreign journalists, human rights workers and academics, making it difficult to verify claims of abuses.
Tobing said Tabuni was on shot Thursday morning when police tried to arrest him near Waena housing complex in Jayapura, the capital of Papua province.
He said Tabuni fought back and grabbed a weapon from an officer before he was shot. He added that Tabuni was suspected in a recent spate of attacks in the province.
Sixteen people, including seven soldiers and police, have been killed in different places in Papua since last month. Four were pro-independence activists.
According to police, following Tabuni's death, a crowd of protesters went on a rampage in Jayapura, many of them carrying machetes and arrows. Police said most of those injured or killed in Thursday's riot were settlers from elsewhere in Indonesia.
Papua, a former Dutch colony in the western part of New Guinea, was incorporated into Indonesia in 1969 after a U.N.-sponsored ballot. A small, poorly armed separatist group known as the Free Papua Movement has battled for independence since then.
Human Rights Watch, however, says the military is responsible for some of the violence. The New York-based group said the government is failing to adequately investigate the killings, and is preventing rights monitors and journalists from going to Papua to see for themselves.
President Susilo Bambang Yudhoyono has conceded that Indonesian security forces have overreacted at times but said the attacks were “on a small scale with limited victims.”