About 1,500 people stormed a house in Banten province on Sunday 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 and has a long history of religious tolerance, but in recent years a hard-line fringe has grown louder and the government — which relies on the support of Islamic parties in Parliament — has been accused of caving in to it.
The latest attacks on Ahmadiyah — which drew rare condemnation from President Susilo Bambang Yudhoyono — were captured on video and circulated widely on national television and the Internet.
The most disturbing clip, posted on YouTube, showed assailants repeatedly pounding two victims — who 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, thought to have 200,000 followers in Indonesia, 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 causal 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 Islamic Defenders Front.
The hardline group pressured local authorities late last year to shutter a Christian church located in a densely populated Muslim area, and assailants stabbed Christian worshipper and beat a minister in the head with a wooden plank as they headed to prayers.
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.