Jakarta – Unidentified attackers raided three remote Christian villages in eastern Indonesia, killing two people, ransacking churches and homes and forcing thousands of people to flee, an official said on Tuesday.

The attacks took place at the weekend on Morotai island on the northern tip of the Moluccas archipelago where more than 5,000 people have been killed in clashes between Muslims and Christians since 1999.

"On Sunday, there were attacks on three Morotai villages. There were churches hit so it seems they're Christian hamlets. The military reported two residents died in one of the villages," said North Moluccas provincial spokesman Said Syafaat Adam.

"We don't know the identities of the victims nor the attackers yet but we're digging into whether this is old vengeance or something else," he told Reuters from the provincial capital Ternate, 2,500 km northeast of Jakarta.

Sporadic religious, ethnic and separatist violence in Indonesia – the world's biggest Muslim country – is a major headache for the government as it tries to convince investors and aid donors it is making progress towards stability.

Adam said at least five churches and hundreds of houses were trashed in the attacks and more than 2,000 people fled from the villages.

He said a lack of communication equipment in the remote villages had impeded an investigation but troops had been sent to the island and the violence had been contained.

The attacks underscore the tension that remains in the once idyllic islands despite a peace deal signed by both sides in February. A civil emergency status, one level down from martial law, is in place in the provinces of Moluccas and North Moluccas.

About 85 percent of Indonesia's 210 million people are Muslim but Christians make up roughly half the population in some eastern areas.