At least 40 lives have been lost in the past few days, according to news reports.
On Sunday, fighting reportedly flared on the island of Haruku, some 1,600 miles east of the Indonesian capital of Jakarta, when a Muslim mob attacked and burned a church, according to a local military official.
Some 600 Christians refugees fled to Bali Friday from the island of Lombok, fearful of a revival of religious violence in the wake of a three-day rampage against Christians that left five people dead.
The attack on Christians followed Muslim protests on the island demanding the Indonesian government put a stop to fighting between Christians and Muslims on the country's eastern Maluku and North Maluku provinces, also known as the Spice Islands. About 2,000 people have died there in in the past year.
Christians once held a small majority in the islands, but an influx of Muslims from other parts of Indonesia changed the area's religious makeup.
During the three-day rampage on the tourist island of Lombok, Christian churches were burned and their homes and businesses attacked by Muslims, according to the Associated Press. The havoc led to the evacuation of hundreds of tourists from the island's resorts.
Seventeen people were hospitalized, victims of riot police.
Anti-Christian protests were also under way in Ambon, Maluku's capital, where protesters demanded the resignation of local military chief Brig. Gen. Max Tamaela. Protesters claimed Tamaela, a Christian, is anti-Muslim.
Indonesian President Abdurrahman Wahid announced earlier this month his intention to replace both Tamaela and the region's Muslim governor, both of whom were perceived as biased in favor of their own faiths, but he has not set a date for the replacement.
Indonesia, a sprawling Southeast Asia island nation, is the world's most populous Muslim nation. Christians comprise a small minority. Over the past year, the inter-religious violence has spread from the Maluku Islands to other parts of Indonesia.