Mobs rioted in a predominantly Muslim quarter of the regional capital, Ambon, and set fire to a van carrying Christians, police said. One person was burned to death, BBC said.
The rioting was apparently triggered by news that three Muslim women had been shot dead on a beach on the island of Sapura.
The Moluccas, about 2,300 kilometers (1,400 miles) east of Jakarta, have been plagued by Muslim-Christian clashes since January 1999. More than 5,000 people have been killed in the violence. Fighting has continued despite a peace accord signed by both communities in February.
On Thursday, three teen-age girls were killed when a homemade bomb went off at a sports center in Ambon. A 20-year-old woman later died of her injuries.
Indonesian Vice President Hamzah Haz blamed the bombing on agitators who, he said, wanted to destabilize the country, BBC reported. He denied the attack was motivated by religious rivalry.