Fabianus Tibo, 60; Marinus Riwu, 48; and Dominggus da Silva, 42, were sentenced to death in 2001. They were found guilty of leading a mob in a 2000 attack that killed 200 people at an Islamic boarding school during Muslim-Christian clashes in Central Sulawesi's Poso region.
"It has been done ... the location was around the airport," a police official who declined to be identified told Reuters. The executions occurred today.
The trio had originally been scheduled to be shot in August. But the execution was postponed after demonstrations by thousands of Indonesians and an appeal from Benedict XVI.
Christian and human rights groups contended that Tibo and his friends were victims of an unfair trial.