Police spokesman Rikwanto said that Bakri Baroncong was believed to have made the explosives for a failed attempt to kill the governor of South Sulawesi province in 2012. Bakri had avoided capture for more than five years and was tracked down at an Islamic boarding school in the province.
Five suspected militants were arrested in Pekanbaru city in Sumatra and two others in Central Java province.
The ninth suspect, Hendrasti Wijanarko, was captured in East Java province. He was linked to four militants convicted over a plot to bomb a guard-changing ceremony at the presidential palace in Jakarta.
Indonesia, the world's most populous Muslim nation, has carried out a sustained crackdown on Islamic militants since the 2002 bombings on the tourist island of Bali killed 202 people, mostly foreigners.
Islamic State group-inspired militants have not made a big impact with their attacks in Indonesia, but officials fear that could change if Indonesians who fought with IS in the Middle East return home.