The men were taken before the firing squad at 12:15 a.m., according to a senior police officer who asked not to be identified because he wasn't authorised to speak to the media. Metro TV and SCTV had similar reports, but did not identify their sources.
The men's execution had been delayed in mid-August after a plea for clemency from Pope Benedict XVI and demonstrations by thousands of Indonesian Christians.
Pope Benedict had called on Indonesia to stop the imminent execution last month, as thousands of Indonesians held a prayer vigil in opposition to the death sentences.
A Vatican spokesman, the Rev. Federico Lombardi, told the Italian
news agency ANSA that news of the execution "was very sad and painful".
Fabianus Tibo, 60, Marinus Riwu, 48, and Domingus da Silva, 42, were found guilty of leading a Christian militia that launched a series of attacks in May 2000 including a machete and gun assault on an Islamic school where dozens of men were seeking shelter.
"I understand they have been killed," said Roy Rening, their attorney, adding that he was still awaiting confirmation from the prosecutor's office.
The men told relatives and a priest during final prayers at their jail Thursday that they were innocent but ready to die.
Authorities in Indonesia denied three Catholic men the right to attend Mass on the day before their execution.
Prison officials refused to allow a priest to hear the men's confessions and celebrate Mass for them one last time on Thursday.
The officials' decision - as well as the refusal to allow the bodies of the three men to lie in state in the Paul cathedral- appears to violate Indonesian law, which stipulates that a prisoner's last wishes should be granted before execution.
