At least 18 people in Indonesia's Papua province are serving jail sentences for peacefully expressing political views, Human Rights Watch (HRW) says.
The rights group said several Papuans had been jailed in recent years for their peaceful support for self-determination for the province.
Opposition to Indonesian rule in Papua has simmered since Jakarta took over from Dutch colonial control in 1963.
An official in Papua denied anyone had been jailed for peaceful protest.
Jakarta has been fighting a low-level insurgency for decades, with small, armed groups carrying out sporadic attacks on economic and military targets in the province.
But there has also been continued non-violent protest from a much wider section of society, the BBC's Lucy Williamson in Jakarta reports.
'Tool of repression'
The Human Rights Watch report highlights the cases of 18 people the group describes as political prisoners.
It includes the case of Filep Karma, a 45-year-old civil servant convicted of rebellion after organising peaceful demonstrations and raising the Papuan flag. He received a 15 year prison sentence.
His case is not unique, HRW said.
"All too often Papuans not involved in the armed insurgency are caught up in anti-separatist sweeps or arrested as troublemakers for peacefully expressing their political views," the organisation's report said.
The courts in Papua are "being used as a tool in political repression", often handing down sentences harsher than those sought by the prosecution, HRW noted.
The organisation calls on Jakarta to immediately release all political prisoners in Papua and to drop any outstanding charges against individuals awaiting trial
The government is also urged to repeal "vague and broad laws", which HRW said enable prosecutions to violate international law.
The head of Papua's Law and Human Rights Department denied that anyone had been jailed for peaceful protest, but said that some people had received sentences for belonging to separatist organisations.