Markus Makur, Timika – Police said Kelly Kwalik, a leader of the separatist Free Papua Organization (OPM), was shot to death during a raid in the early hours of Wednesday morning.
Papua Police spokesman Sr. Comr. Agus Riyanto said the Papuan rebel leader was cornered in the Gorong-Gorong complex, one of his hideouts in the town of Timika, Mimika regency.
Kelly was shot in the right thigh by Mobile Brigade police as he was attempting to escape a house in the complex at around 3 a.m., Agus said.
He said Kelly died from blood loss after being taken to the Kuala Kencana clinic for treatment. At least five people were arrested in the raid.
Agus said police had planned to arrest the rebel leader. However, it was not immediately clear what police intended to charge him with.
Earlier this year Papua Police held a meeting with Kelly in connection with a series of attacks on US-based gold miner PT Freeport Indonesia in Timika.
During the talk, Kelly claimed he was not responsible for the attacks, which killed three people and injured dozens of others since the first ambush on July 11.
Police have denied allegations they had set up the talk to establish that native Papuans were behind the violence. At least seven Mimika residents are facing trial in Jayapura for the attacks by unidentified gunmen.
Later in the day, security authorities flew Kelly's body to the Papuan capital of Jayapura for DNA testing to verify the body's identity.
On board the same police plane were Papua Police deputy chief Brig. Gen. Syafei Aksal, Mobile Brigade deputy commander Godhelp C. Mansnembra, and a number of other local high-ranking officers.
Police said they were adamant that the body was that of Kelly, but were conducting the tests as part of procedure.
Separately, hundreds of members of the Amungme tribe occupied the Mimika regency legislative council office following the incident. They demanded police return Kelly's body, saying they would bury him in Timika.
The protesters tried to block the Moses Kilangin Airstrip to prevent the police from flying the body to Jayapura. But they failed to break through a police cordon at the airbase.
Police performed roadside stops on motorists heading to the airstrip and to the nearby hamlet of Kwamki Lama as a precautionary measure.
By late afternoon, the Papuan demonstrators still occupied the legislative council. Mimika council speaker Trifena M. Tinal came out of his office and negotiated with the protesters, calling on them to disperse.
Amid the protests, authorities tightened security at check point entry 28 into the Freeport mine and the company's Kuala Kencana clinic.
An expert on Indonesia at Australia's Deakin University, Damien Kingsbury, told Reuters that Kelly's death could potentially improve prospects for talks between the wider separatist movement in Papua and the government. "[Kelly] was the most militant of the senior OPM figures," he said.