National police chief Sutarman said there were indications that militants were heading to areas they wished to target, and may be assembling bombs.
"The terrorists have cells everywhere and they are active. We are continuing to pursue them," Sutarman, who like many Indonesians goes by one name, told reporters in Jakarta.
He did not give details about any of the suspected terror groups.
Indonesia's small Christian minority has come under increasing pressure in recent years from Islamic hardliners, who have forced the closure of churches and protested outside places of worship.
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Most such terror attacks in recent times have been low-level and targeted police.
Since 2000, when improvised bombs disguised as Christmas gifts delivered to churches and clergymen killed 19 people and injured scores more across Indonesia, police have gone on high alert at the festive season.
But officials rarely give such specific warnings as that issued today.
Sutarman said that as well as the capital, militants were thought to be targeting central Sulawesi island, parts of which are known as a terror hotbed, and other regions which he declined to name.
He added that police were monitoring the suspected terror cells and would only move against them when their plans were thought to be at an advanced stage.
Indonesia has waged a crackdown on Islamic militant networks over the past decade after attacks on Western targets, including the 2002 Bali bombings which killed 202 people, mostly foreign tourists.
The crackdown has succeeded in dismantling groups seen as a major threat although small terror cells still exist.