The Christian minority in the world's most populous Muslim nation is on a state of high alert, with many saying they are too frightened to go to church despite the heavy security presence.
An explosion in a residential area of south Jakarta on Monday added to the tension, but the cause was not immediately known.
Christmas Eve bombings at churches in Jakarta and other cities and towns last year killed 15 people and injured dozens.
The American Embassy in Jakarta last week advised its citizens to keep a low profile and warned that another wave of bombings was possible.
"There are indications that similar incidents could occur again this year," the embassy said.
However, some political analysts doubted there would be fresh violence, saying last year's bombings were aimed at destabilising the government of former President Abdurrahman Wahid.
Mr Wahid, who was trying to push through democratic reforms after three decades of authoritarian rule, was ousted in July and replaced by Megawati Sukarnoputri.
Jakarta police spokesman Colonel Anton Bachrul Alam said more than 9,000 officers would be stationed at churches in the capital and thousands more would guard places of worship in other cities.
He said Indonesian Muslim groups were also helping to safeguard Christians attending
Christmas Eve services, including members of the radical Front for the Defenders of Islam.
The latest explosion was reported to have damaged part of a boarding house in south Jakarta. There were no reports of casualties.
News agency AFP quoted witnesses saying the blast occurred next to a house which was hit by an explosion in June.
Police spokesman Saleh Saaf said on the SCTV network that the blast was believed to have been caused by explosives which had remained undiscovered following the earlier incident.
Security advice
But BBC South-East Asia correspondent Jonathan Head says the explosion is bound to make Christians even more nervous, just a few hours before many of them attend mass on Christmas Eve.
No one has yet been convicted for carrying out last year's Christmas bombing campaign but police have arrested several suspects.
Our correspondent says that with Muslims and Christians still engaged in bitter communal fighting in eastern Indonesia, authorities want to avoid any incidents which might provoke similar conflict in other parts of the country
Police have advised churches to install metal detectors and to watch for any unfamiliar faces among their congregations.
At least three churches have been targeted by bombers in Jakarta in the past two months, although there have been no fatalities.