National police spokesman Sulistyo Ishaq said Wednesday anti-terror operations also netted bomb-making materials, weapons and ammunition.
He says explosive devices found in the Tuesday raids were a sophisticated version of those used in the 2004 Australian Embassy bombing in Jakarta.
A manhunt was continuing for two other suspects.
One of those already in custody, Wahyu Ramadhan, was renting a house up the road from the country’s largest fuel depot.
The men are believed to have ties to Jemaah Islamiyah, the Southeast Asian terror group blamed for a series of bombings in Indonesia that have killed more than 240 people.