Two of those arrested are identified as Herman and David, while the identity of the third remains unknown.
A team of police officers, assisted by a bomb-defusing squad, is still combing the scene in a search for possible bombs. A number of articles have been seized from the suspects as evidence.
Police officials, however, were not available for comments about the arrests.
The three suspected terrorists are natives of Gang Haji Kimin at Palmerah Barat Street 2 in Palmerah district, West Jakarta, according to Prawitno, a local resident.