At least 200 people were arrested in several cities in Papua and Java, said Veronica Koman, a lawyer for Papuan independence activist Filep Karma.
Today is the 55th anniversary of the official declaration of an Indonesian military campaign to take control of Papua from the Dutch.
Koman said several people were arrested last week when they applied for demonstration permits.
She said the headquarters of the pro-independence National Committee for West Papua in Jayapura, the capital of Papua province, was vandalised during a police raid today.