Amnesty International has urged the US President, Barack Obama, to raise human rights issues when he meets his Indonesian counterpart, Susilo Bambang Yudhoyono, in Jakarta, in two weeks.
Amnesty says Indonesian authorities continue to use repressive legislation to criminalise peaceful political activities.
It says violations of this right are particularly severe in areas where there has been a history of pro-independence movements such as Maluku and Papua.
Amnesty says it would like President Obama to press for the release of political prisoners, such as Filep Karma and Yusak Pakage, who are serving prison sentences of 15 and 10 years respectively for peacefully raising the Papua flag.
It says impunity continues to be a serious problem in Indonesia to this date as there have been no convictions for the killing of tens of thousands of people in East Timor.