The Indonesia news agency, Antara, says police in Mimika in the Papua region are holding six people who were involved in unfurling the Morning Star flag on Saturday December the 1st.
That day is commemorated by Papuans as the day the region declared itself independent of its former Dutch colonial masters.
The identities of the six have not been revealed but police say two had been carrying ammunition.
A further thirty people taken into custody and questioned were all released by Sunday.
The police confiscated a Morning Star flag and a tree trunk that was used as the flag pole.