Despite the presence of hundreds of riot police in Lombok's capital and a nearby tourist resort, roaming gangs of youths torched houses and shops in the town.
In the capital, one of the largest churches, the Immune Protestant Church, was left looted and charred, obscene graffiti daubed on its walls.
"Be afraid pastor, the Muslims will drink your blood," was scrawled across the entrance. The words "public toilet" were written where an altar once stood.
Police said three people were fatally shot in the unrest that erupted Monday, following a Muslim protest against the government for failing to curb violence between Muslims and Christians in the islands that were collectively known as the Spice Islands during Dutch colonial rule.
Fighting in the islands, where Christians once held a slim majority, has cost 2,000 lives in the last year. An influx of Muslims from Indonesia's other islands in the past two decades has changed the area's religious makeup and fueled tensions.
About 90 percent of Indonesia's 210 million people are Muslims, making it the world's most populous Islamic state.
Many Indonesians fear the unrest in the Spice Islands signals the advent of a wider sectarian conflict that could engulf the entire country - the world's fourth most populous.
President Abdurrahman Wahid, a moderate Islamic leader, has condemned growing calls for a holy war, or "jihad," against the Christian minority, but is seemingly powerless to prevent the violence from escalating.
Speaking to his Cabinet in Jakarta, Wahid said he had received reports that some military and government officials had instigated recent violence.
"The president has ordered military leaders to investigate this matter thoroughly and immediately," said Cabinet Secretary Marsilam Simanjuntak.
Meanwhile, senior security minister Gen. Wiranto told reporters that the violence was under control and that it "will not spread to other regions."
There has recently been local media speculation of a deep rift between Wiranto, Indonesia's former military commander, and Wahid.
Lombok, a picturesque volcanic island of palm-fringed beaches and green rice fields, is home to Indonesia's three main faiths. Although most of its people are Muslim, there are minority groups of Hindus and Christians.
Gangs of Muslims manned roadblocks on roads leading out and checked the identification papers of all motorists in an apparent attempt to prevent Christians from fleeing.
The local airport was crowded with nervous Christians trying to leave for the neighboring island of Bali, Indonesia's premier tourist destination.
About 3,000 Christians have reportedly sought refuge in military and police bass on Lombok, 670 miles east of Jakarta.
Resort hotels organized the evacuation of hundreds of foreign tourists when the violence started. There were no reports of injuries or damage to the hotels, although two restaurants were set ablaze by the mobs.
Many hotels and shops in the area posted signs at their entrances to indicate Muslim ownership.
In Solo, a town in central Java province, 2,000 Muslims gathered to threaten a holy war if the government does not put an immediate end to the violence. In Jakarta, 100 people attended a similar protest at the office of Vice President Megawati Sukarnoputri.
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