The Jayapura demonstration was one of more than 14 rallies in Indonesian cities, calling for West Papuan rights to self-determination to be respected.
More than 500 people were reported to have been arrested for participating in the rallies.
While the vast majority were released later in the day, two arrested in the Papua provincial capital have been charged.
Hosea Yemo and Ismael Alua are reportedly members of the West Papua National Committee, (KNPB), and the pro-independence representative group which organised some of the rallies.
