Yeremia Zanambani was shot dead last month, one of a series of killings in Papua's Intan Jaya regency.
The pastor was killed while tending to his pigs, two days after a pair of Indonesian soldiers were killed by what the team called an armed criminal group, the government's oft-used term for the West Papua Liberation Army.
The Liberation Army's guerilla fighters are engaged in ongoing conflict with Indonesia's military in Papua's rugged interior.
The team said it found indications that Indonesia's security forces were involved in the shooting of Pastor Zanambani.
However it also said there was a possibility that a third party was involved in the killing, which has sparked outrage in Papua region.
Indonesia's Co-ordinating Political, Legal and Human Rights Minister, Mahfud MD, said the government would follow up on the findings.
According to him, this would include ordering the National Police and Attorney General's Office to solve cases such as the killing of the pastor by following the applicable criminal and state administrative laws.
The Jakarta Post reports the minister saying he would also pass on the findings to the National Police, the Indonesian Military and the State Intelligence Agency for further investigation.
Furthermore, Mahfud recommended that the government equip vulnerable communities with better security to provide safety to locals.
Photo supplied Caption: Yeremia Zanambani