National police spokesman Brig. Gen. Anton Bachrul Alam said Tuesday that Heru Kuncoro was captured June 9 in Pekalongan in central Java.
He is among the 16 people arrested in recent days on suspicion of plotting cyanide attacks against police.
Police say Kuncoro was a facilitator who purchased electronic equipment for the 2002 bombing on the tourist island. He fled to the Philippines in 2003.
Before the Bali bombing, he took part in paramilitary training in Maluku during a sectarian war between Muslims and Christians in which up to 9,000 people died between 1999 and 2002.