Events held in the cities of West Papua to mark the anniversary of the Papuan nationalist day mainly took the form of prayer events.
Yesterday was the 55th anniversary of a declaration of independence by the indigenous people of the former Dutch New Guinea declared independence.
The Papuan nationlist Morning Star was subsequently banned when Indonesia took over, but each year global rallies mark this anniversary in support of Papuans.
In Papua, the biggest of yesterday's events was in the Highlands town of Wamena where 3000 people converged for a large prayer event at the Traditional Council headquarters.
Benar News reported that organisers of the event thanked the Indonesian authorities for permitting the opportunity to worship.
Among the speakers at another peaceful event, across in Papua's provincial capital, was Filep Karma.
Mr Karma was released from prison a year ago after serving eleven years for raising the Morning Star in 2004.
At the Jayapura event, hundreds signed a petition in support of the United Liberation Movement for West Papua with its growing representative role in the Pacific region.
Unlike December 1st demos in global centres such as London, Sydney, the Papua events were not allowed to feature raising of the Morning Star.
"Papuans are already aware and do not want to be provoked by violence and conflict," Mr Karma was reported as saying.
"Prayers and speeches such as these show political maturity and a dignified struggle."
The event also heard a speech written by the Liberation Movement secretary-general Octo Mote.
He said Indonesians "are starting to acknowledge that crimes have been committed by the government and military of Indonesia in Papua".
In Jakarta police arrested over two hundred people for participating in a demonstration in support of West Papuans' right to self-determination.
14 were arrested in the other Indonesian city of Yogyakarta.