The bodies, which witnesses said were burned beyond recognition, were found in Larat, a village on the island of Kai Besar in Maluku province, the Antara news agency said.
More than 250 people have been killed and hundreds of buildings burned in Maluku, most on the island of Ambon, since bloody clashes first erupted between Christians and Muslims in January.
Fighting broke out in the islands southeast of Ambon on Wednesday and has since left 60 dead. The military said Muslims killed two Christians on Sunday in Tual, near Kai Besar, 1,750 miles east of Jakarta.
More than 13,000 people have already fled their homes, seeking shelter in government and military installations in Tual.
Local military chief Lt. Col. Ery Susanto said the navy would send several warships to the region to avert an exodus of frightened residents.
Indonesia is the world's most populous Islamic country. Nearly 90 percent of its 210 million people are Muslims. However, Maluku has a large Christian population.
The violence in Maluku comes amid Indonesia's worst economic crisis in decades as well as political uncertainty that has followed the resignation of authoritarian President Suharto last May.
Ethnic and sectarian unrest has broken out in several parts of the archipelago nation. Last month more than 200 people were killed in ethnic fighting on the island of Borneo.
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