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Bomb squads swept churches for explosives and security guards dressed as Santa Claus searched cars after police warned that al-Qaida-linked terrorists could be plotting Christmas terror attacks.
Thousands of troops were also on guard.
Though most of Indonesia's 190 million Muslims practice a moderate form of the faith, attacks against Christians and Westerners have increased in recent years amid a global rise in Islamic radicalism.
Suicide bombings and at least three recent beheadings have put many on edge.
Maj. Gen. Firman Gani, the Jakarta police chief, said Saturday that Jemaah Islamiyah terrorists "could carry out" an attack on Christmas to retaliate for the death last month of bomb-making expert Azahari bin Husin, who was gunned down in a police raid.
Jemaah Islamiyah was blamed for near simultaneous Christmas Eve church bombings in 2000 and five suicide attacks targeting Western interests since then - including the October 1 restaurant strikes on the resort island of Bali.
Together, more than 260 people have died, many of them foreign tourists.
Some 47,000 soldiers and police have been deployed nationwide to guard houses of worship, hotels, clubs, restaurants and shopping centers.
Even security guards dressed as Santa Claus were taking part, searching beneath cars for explosives at the glitzy Mandarin Oriental Hotel in Jakarta.
Police Lt. Sulianto said 80 bomb squads were sweeping churches in the capital and in the neighboring cities of Bekasi, Tangerang and Depok hours before midnight Mass. The ceremonies proceeded without incident nationwide, security officials and religious leaders said.
The United States, Australia and several other governments have urged their citizens against travel to Indonesia over the holidays, saying the chance for a terror attack is very high.