The New York-based rights watchdog group, Human Rights Watch, says Indonesian jails hold at least 100 political prisoners from the Papua and Moluccas regions, and some have been tortured.
The body has called on the Indonesian government to release prisoners detained for their political views and repeal laws allowing authorities to jail peaceful protesters for treason or rebellion.
It also urged the government to revoke laws banning the display of logos and flags.
The report says the practice of lumping together peaceful advocates and armed militants and treating both as criminals continues in Papua and the southern Moluccas.
