Indonesian military officials have also initiated an investigation into the six officer’s involvement in the killing, lieutenant general Chandra W Sukotjo said on Monday.
Senior military official Teguh Muji Angkasa said the country’s military and police will carry out a joint investigation into the killings.
The soldiers have been accused of luring the victims into meeting them with a promise of selling them weapons but later killed them, according to police.
The Indonesian soldiers also dismembered the civilians bodies, stuffed them into sacks and disposed of the remains into a river near the city of Timika, officials said.
“We have been given the order to investigate the incident,” Mr Teguh said, adding that the soldiers will be sternly sanctioned if the findings of the investigation showed their involvement in the barbaric killing.
The top military official added that the victims had been negotiating purchase of weapons with the arrested Indonesian officers on 22 August but the deal went sour.
Officials have not named the six suspects.
Indonesia gained territorial control of the former Dutch colony Papua two years after it was declared independent in 1961 and has maintained a heavy military presence in the region since.
The southeastern nation has deployed heavy military battalions in Papua and faced clashes from small groups of separatist fighters who have stirred a low-scale insurrection on the island nation seeking independence from Indonesia.
The Indonesian military has faced accusations of human rights abuses in Papua and officials have rarely initiated investigations into the incidents.
Spokesperson for separatist group West Papua National Liberation Army (TPNPB) Sebby Sambom has asked the government to hold the perpetrators accountable or risk further violence.
“If Indonesian president Joko Widodo does not immediately take responsibility, then the TPNPB together with the Papuan people will take revenge,” Mr Sambom warned on Monday.
One of the victims was also linked to the TPNPB, Papuan police officials said.
Armed conflict in Papua has surged significantly since 2018, with attacks by the TPNPB becoming deadlier and more frequent, a report by the Jakarta-based Institute for Policy Analysis of Conflict said in July this year.