Their lawyer said he had been informed of the executions of Fabianus Tibo, Dominggus Da Silva and Marianus Riwu by the prosecutor's office in the town of Palu.
Roy Rening said: "They have been executed. Their bodies are now undergoing an autopsy at the police hospital."
The three were convicted in 2001 of leading a Christian group that carried out violence against Muslims in religiously-divided Central Sulawesi province in 2000, although they denied they were behind the unrest.
More than 1000 were killed in the region between 2000 and 2001 when Muslims and Christians clashed.
Rening added that he refused to be present at the deaths to protest against a rejection by the state of their last demands, including that their bodies be flown back to their home towns or laid in wake at Palu's main Catholic church.
The trio were initially scheduled to be shot last month but authorities granted a last-minute reprieve - even following the preparation of their coffins - shortly after Pope Benedict XVI issued a plea for clemency, although authorities denied that there was a link between the pope's plea and the reprieve.
Federico Lombardi, a Vatican spokesman, said the execution of the men was "very sad and painful news. Every time capital punishment is used is a defeat for humanity".
The human rights group Amnesty International said there were serious doubts about the fairness of the trials.
Isabelle Cartron, the group's Southeast Asia researcher, said: "We are deeply disappointed that despite the debate on the death penalty that the case had sparked across Indonesia, the state went ahead and killed these three men."
Cartron noted that there were concerns about defence witness testimony being ignored by the court as well as the intimidation of the men's lawyers, who endured death threats and a bomb being planted at one of their homes.