Brigadier General I Gusti Putu Danny Karya Nugraha, who was the chief intelligence official in Papua, was killed in an ambush by the West Papua Liberation Army in Puncak, in the central Highlands, on Sunday. The independence group has claimed the general's killing.
"He was in the area as part of the operation to restore security and to boost the morale of locals in the region following a series of attacks by separatist and terrorist groups," Wawan Purwanto, a spokesman for the National Intelligence Agency said.
Few details have been given, and verifying details from Papua's interior is always difficult. But it is known that the general was with a small group of soldiers and police officers when he was killed near a church in remote Dambet Village.
In announcing the general's death at a news conference in Jakarta on Monday, Indonesian president Joko Widodo - flanked by his vice-president and heads of the military, police and state intelligence - vowed a military crackdown in Papua.
"I emphasise that there is no place for armed criminal groups in Papua or any other part of the country," Joko said. "I have ordered the military and police chiefs to pursue and arrest members of the armed criminal group."
Bambang Soesatyo, the speaker of the People's Representative Council, one of Indonesia's houses of parliament, later endorsed a crackdown on rebel groups, saying: "Destroy them first, we will discuss human rights later."
It appears calls for a crackdown are being heeded. On Thursday, police in Papua claimed that 10 people - nine rebels and one police officer - were killed in an hours-long gunfight in Puncak district as personnel hunted down those responsible for Gusti's death.
Veronica Koman, a Papuan human rights lawyer based in Australia, said she understood 19 villages near the scene had been cleared by military on Thursday, with villagers forced to flee.
The region has seen an increase in conflict between separatist groups and rebels this month, and the killing of a top military figure is likely to be the catalyst for further escalation. That has human rights groups worried that civilians and the indigenous Papuan population will bear the brunt of the conflict, caught in the fire, crossfire, retaliation and aftermath, as has often been the case in this conflict that has played out for more than 50 years.
"What's dangerous is the comments by Indonesian leaders [and] public officials that encourage retaliation," she said. "It's as if the Indonesian military and police have now licence to kill as they justify their revenge."
Papua takes up the western half of the island of New Guinea and was occupied and annexed by the Indonesians in the 1960s. The regions of Papua and West Papua have a degree of autonomy, but many Papuans have been calling for a referendum on full independence, with separatists waging a low-level insurgency campaign.
Koman said an escalation in violence was not the answer.
"Jakarta should finally try another approach in this conflict," she said. "Even if Jakarta can completely kill the fighters in the jungle, there will a new liberation army created. Sit down and talk to West Papuan representatives in equal footing and dignity.
"At the end of the day it's the civilians again who suffer the most."
Photo: Supplied caption: Arrival of more Indonesian troops in Jayapura, Papua, March 2021