About 1,500 people stormed a house in Banten province over the weekend to stop 20 Ahmadiyah followers from worshipping. They killed three men and badly wounded six others, while destroying the house and setting fire to several cars and motorbikes.
Indonesia is a secular country of 237 million people with more Muslims than any other in the world.
Despite a long history of religious tolerance, a hard-line fringe has grown louder in recent years and the government - which relies on the support of Islamic parties in Parliament - has been accused of caving in to it.
Rights group said Tuesday a 2008 decree that bans religious activities of Ahmadiyah, thought to have 200,000 followers in the archepeligic nation, should be immediately revoked. They say it only encourages violence.
The latest attacks on Ahmadiyah - which drew rare condemnation from President Susilo Bambang Yudhoyono - were captured on video and have circulated widely on national television and the Internet.
The most disturbing clip, posted on YouTube, showed assailants repeatedly pounding two victims - who had been stripped naked and appeared to be dead - with heavy sticks.
A policeman came to the scene but his screams of "stop" were almost inaudible among dozens who shouted "Allahu Akbar" or God is Great.
The Ahmadiyah are considered deviant by many Muslims and are banned in many Islamic countries because they believe that Muhammad was not the final prophet.
"I have ordered a comprehensive investigation to find out the real cause of the incident so that those guilty, or violating the law, can be penalized," Yudhoyono told a news conference.
He also called on security forces as well as local governments to be proactive in taking action against the instigators of such violence.
"Don't wait until the conflicts and clashes have already happened," Yudhoyono said.
Many attacks on religious minorities in recent years have been carried out by members of the hardline Islamic Defenders Front, known also for smashing bars and attacking transvestites and anyone one else considered "blasphemous" with bamboo clubs and stones.
The group pressured local authorities late last year to shutter a Christian church located in a densely populated Muslim area, and assailants stabbed a Christian worshipper and beat a minister on the head with a wooden plank as they headed to prayers.
Thirteen members of the Islamic Defenders Front have gone on trial in the case, and state prosecutors on Monday sought a six-month prison term for Murhali Barda, a local group leader, for instigating the Sept. 13 attack.
The Setara Institute for Peace and Democracy, a human rights group, says attacks on religious freedom by hard-liners are steadily increasing.
It says in 2010 there were 64 incidents, ranging from physical abuse to preventing groups from performing prayers and burning houses of worship, up from 18 in 2009 and 17 in 2008.
Ahmadiyah attack: http://tinyurl.com/6gd3qtb