No bibles were burnt in an incident last week which preceded unrest in the Papua provincial capital Jayapura, according to Indonesian officials.
On Thursday a riot occurred after members of a local Zionist congregation clashed with local security forces on the main road to Abepura district.
When people heard that bibles were being burnt at a local military barracks, an angry mob gathered near the premises to protest, blocking the main road.
Five people were injured in the ensuing melee, as the mob threw projectiles at security forces, and soldiers fired shots to disperse people.
But a statement from the Minister Counsellor at the Indonesian Embassy in Wellington, Wanton Saragih, said no Bibles were burned, either deliberately or accidentally.
Mr Saragih cited the Chairman of the Papuan Synod of the Indonesian Christian Church, Reverend Dani Mita, regarding the incident.
According to Reverend Mita, the riot was triggered by video and photographs spread by irresponsible persons purporting to show that a policeman had burnt Bibles.
He said the policeman was merely cleaning an area by burning paper rubbish in a concrete rubbish bin at the back of the barracks.
The church leader said the only thing burnt accidentally was a book on the history of religion titled Asal Usul Agama-Agama (Origin of Religions) written by Thomas Hwang.
After the crowd was dispersed in the afternoon, police arrested two men suspected of organising the unrest, Jhony Lee and Fauk Tukayo.