Carrying banners demanding "freedom" and calling for international attention, the Papuans tried to march on the provincial parliament building but were blocked by Indonesian police.
"We refuse the 1969 referendum and urge the Indonesian government to organise a new referendum of independence for Papuan people," protest coordinator Bucktar Tabuni said.
One speaker told the crowd through a megaphone: "Our children weren't born to be tortured and killed by Indonesia's security forces. Our only wish is for Papuans to be treated well as human beings."
The October 16 Jakarta Post, that Indomnesian police are questioning several witnesses after the West Papuan Morning Star flag (Bintang Kejora) was "raised in four strategic locations in Nabire regency, Papua" on October 15.
The flags, associated with the Free Papua Movement (OPM) and banned by the Indonesian occupation forces, were hoisted at the Legislative Council and Regency offices, the Kalibobo market and Nabire's tourism office at around 3 am local time, the Jakarta Post reported.
"We have questioned five witnesses. We have not identified any suspects so far," Nabire police chief Adjutant Senior Commander Rinto Jatmono told the Jakarta Post.
Rinto said the flags were probably raised during an unexpected electricity blackout which struck the regency after heavy rain. "The flags were brought down at about 5 am," he added.
Separately, Nabire Military District Commander Lt. Col. Jansen Simanjuntak said his officers discovered the flags had been hoisted while they were patrolling the areas.
He said his officers then lowered the flags and brought them, along with two witnesses, to military district headquarters.
"We then handed the witnesses over to the police. The number of witnesses may increase," Jansen said.
Meanwhile, Manokwari District Court has reportedly sentenced 11 suspects to eight months in jail for flying separatist flags in the regency on March 3 and March 13 this year.
The 11 hoisted the flags during rallies protesting government regulation 77/2007 which banned the display of "separatist flags".
The Papua Customary Law Council has drafted a special regulation recommending that the Morning Star flag be used as the provincial symbol, and submitted this to the Papua People's Representative Council.
Indonesian human rights activists, including former Indonesian President Abdurrahman Wahid (Gus Dur), have urged the Indonesian government not to criminalise the display of such flags, saying they are merely a form of cultural expression.
Tempo aslo reported that the banned Morning Star flag was raised in a dormitory for Papuan students in Yogyakarta.
A spokesman for a Papuan student association in Yogyakarta, Roy Liqua, said the flag was raised to coincide with the inaugural meeting of International Parliamentarians for West Papua in London.
Students also said the flag was raised simultaneously in several region in the country, and they were planning an action in Jakarta.