Papua Police have charged two people for allegedly inciting a riot in Tolikara district, which saw a small mosque burn to the ground and triggered widespread fears of sectarian violence across Indonesia.
Police identified the suspects as 26-year-old local bank employee, and a 31 year-old civil servant.
Papua Police chief Inspector General Yotje Mende told the Jakarta Post the two were seen provoking the assault
The pair are charged with inciting others to commit crime under Indonesia's Criminal Code and could face a maximum sentence of five years in prison if convicted.
The two suspects were apprehended in Tolikara district capital Karubaga on Thursday and were flown to Jayapura the following day where they will face more questioning.
Police suspected the two had provoked a group of around 200 people to pelt stones and set fire to shops owned by Muslim migrants in Karubaga during the Islamic Idul Fitri holiday.
Investigators also claimed they have obtained video footage of the pair during the riot.
Violence erupted in Tolikara last week after members of the Evangelical Church of Indonesia - the largest religious group in the district - complained about the use of loudspeakers during a mass Idul Fitri prayer and called for the event to be cancelled.
Witnesses say police opened fire at protesters, killing one and injuring 11 others, although the exact nature of the shooting has been widely contested by the church.
But correspondents say there is no dispute that the shooting led to the riot.
Scores of officials and religious groups, both Muslims and Christians, immediately called for peace out of fear that violence might spread to the rest of the Muslim-majority country, which saw a brutal string of sectarian conflicts between 2000 and 2005.
The National Police chief has instructed officers across the archipelago to counter the spread of provocative messages circulating in the aftermath of the incident.
Meanwhile, police in Jakarta have stepped up security to prevent Papuan students and churches from becoming a target of hate crimes.