National Police spokesman Rikwanto told MetroTV that the residential neighborhood has been evacuated.
He said one person was arrested in the raid.
Police believe those involved in the plot are linked to several militants arrested December 10 in another neighborhood on the outskirts of Jakarta who were planning a suicide bomb attack on a guard-changing ceremony at the presidential palace the next day.
Indonesia has carried out a sustained crackdown on Islamic militants since the 2002 Bali bombings that killed 202 people.