Indonesian officials say no bibles were burnt in an incident last week which preceded unrest in the Papua provincial capital Jayapura.
On Thursday members of a local Zionist congregation clashed with local security forces in 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 as the mob threw projectiles at security forces, and soldiers fired shots to disperse people.
The Minister Counsellor at Indonesia's Embassy in Wellington, Wanton Saragih, said no Bibles were burned.
Mr Saragih said 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 rubbish bin at the barracks.