The New York-based Human Rights Watch (HRW) says there has been a steady rise in attacks on Christians, Buddhists and Muslim minorities.
Many of these were carried out by Islamist militants, it added.
The government says religious harmony is strong in Indonesia, which has a large Sunni Muslim majority.
HRW said it researched its report between August 2011 and December 2012, interviewing more than 100 people of varied religious beliefs.
It included examples of attacks faced by various minority groups, including a mob attack by Islamist militants on the Ahmadiyah religious minority group in 2011 which is said left three men dead.
The report said that "harassment and intimidation of minority communities by militant Islamist groups has been facilitated by the active or passive involvement of Indonesian government officials and security forces".
Those responsible for the attacks received little or no punishment, it says.