Carrying banners demanding "freedom" and calling for international attention, they tried to march on the provincial parliament building but were blocked by police.
"We refuse the 1969 referendum and urge the Indonesian government to organize 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."
Many Papuans accuse Jakarta of stealing the rugged, largely undeveloped province's natural resources. Indonesia's military is also accused of rights abuses and corruption, especially around foreign-owned mines.