Abu Wardah Santoso was one of two militants killed in the shootout Monday, Coordinating Minister for Security, Political and Legal Affairs Luhut Binsar Pandjaitan told reporters. The other was an extremist known as Mochtar, not Santoso's deputy Basri, as police had initially thought.
Santoso, who headed the East Indonesia Mujahideen militant group that claims allegiance to the Islamic State group, had eluded capture for more than five years.
More than 2,500 security personnel, including elite army troops, intensified their operations this year in Poso, a mountainous district of Central Sulawesi province considered an extremist hotbed, to try to capture Santoso and his followers.
The bodies were identified at a police hospital in the capital of Central Sulawesi.