Local police chief Lt. Col. Alex Fauzy Rasyad said about 1,500 people - many with machetes, sticks and rocks - attacked about 20 members of the Ahmadiyah Muslim sect who were visiting their leader in his house in Banten province on Indonesia's main island of Java.
He said the crowd demanded that the sect members stop their activities, but the request was rejected. As a result, the crowd stabbed to death at least three men, destroyed the house and set fire to their cars and motorbikes.
Six others were hospitalized, four with critical injuries.
The police were called, "but the attackers came faster," Rasyad said.
The attack was the latest targeting the Ahmadiyah sect in Indonesia, the world's most populous Muslim nation. Many Muslims see followers of Ahmadiyah as holding heretical beliefs.
Indonesia is a secular country with 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 Islamic Defenders Front 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.
Ahmadiyah, believed to have 200,000 followers in Indonesia, is considered deviant by most Muslims and banned in many Islamic countries because of its belief that Muhammad was not the final prophet.