"They have been executed. Their bodies are now undergoing an autopsy at the police hospital," the men's lawyer Roy Rening said, according to a News report.
Mr Rening said he was informed of the executions of Fabianus Tibo, Dominggus da Silva and Marianus Riwu by the prosecutors' office in Palu, the capital of religiously-divided Central Sulawesi province, where the men were being held.
Mr Rening said he refused to be present at the deaths to protest a rejection by the state of their last demands, including that their bodies be flown back to their hometowns or laid in wake at Palu's main Catholic church.
He was unable to give further details about the precise time of the death, but a flurry of activity had occurred around midnight local time (0400 AEST) at the tightly-guarded jail, where a steady rain drizzled overnight.
"It has been done... the location was around the airport," an un-named police official told Reuters, adding that the bodies had been taken to a police hospital.
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 Benedict XVI issued a plea for clemency, though a link was denied.
Tibo, da Silva and Riwu were convicted of leading a Christian militia that carried out attacks against Muslims in the province, but they categorically denied they were the masterminds behind the unrest.
The case of the three poor farmers drew international concern from rights activists, who criticised the fairness of their trial and saw the men as scapegoats targeted while few others were convicted over the violence that began six years ago, leaving those most responsible on the run.
On Thursday, the men had met for the last time with their relatives, their priest and their lawyer, Mr Rening, who criticised authorities for declining to meet their final requests.
"They should just do the execution and return their bodies to the family... This is a new crime, and I protest this attitude," Mr Rening said.
Typically authorities do turn bodies over to families after executions, following a routine autopsy. Authorities may be concerned that the bodies could become a focal point for protest.
The men's priest, Fr Jimmy Tumbeleka, said he was concerned that a refusal to hand over the bodies could "trigger more anger from the family and others" in the province, where Muslims and Christians live in roughly equal numbers.
More than 4000 security forces have fanned out across the province in the past two days in anticipation of the executions.
Christian leaders had urged their faithful to stay calm and refrain from any violence ahead of the executions, with widespread prayer services for the men being held.
The executions were carried out just a few days ahead of Ramadan, the Muslim holy month of fasting which is expected to begin this weekend.
According to Amnesty International, which had raised questions about the fairness of the men's 2001 trial, the most recent previous execution in Indonesia was in May 2005.
Last requests refused
Indonesian agency Antara adds that the Central Sulawesi public prosecutor's office rejected all of the men's four last requests.
The prosecutor's rejection was disclosed by Fr Tumbelaka after he had visited the Central Sulawesi public prosecutor's office where he was received by a member of the execution team, Agus Setiawan.
The men had earlier made their requests through Fr Tumbelaka including a request that their bodies be laid in state at Palu's main church for one day before burial.
Tibo and Marinus had also asked that their bodies be buried in Beteleme village, Morowali district, while Dominggus wanted his body returned to his family in Flores for burial there.
The inmates also asked that their execution be witnessed by Joseph Suwathan, a bishop from Sulawesi, Fr Tumbelaka, Fr Melky Toreh (from the main church in Palu) and their lawyer, Mr Rening.
Their fourth request was that they be allowed to convey a special message to President Susilo Bambang Yudhoyono through mass media.
All of their requests were rejected by Prosecutor Agus Setiawan who said the authority to handle the convicts up to their burials was in the hands of the state.
Catholic World News adds that the men's requests for a last Mass and Confession were also refused.
Confusion and secrecy
The family of the three men had said earlier yesterday that they had yet to receive official information about the imminent execution of the trio, Central Sulawesi Christian Church Synod chairman Rev Rinaldy Damanik said on Thursday.
Robert Bala Keitimu, a lawyer from the Indonesian Justice and Peace Advocacy Service (Padma), said in Batam on Wednesday that the families of the three death row convicts had at that time received no official information on the date of the execution.
"We knew from the media that Tibo and his friends are to be executed but have so far not received any official information from the Palu District Court," Mr Keitimu said.
Reports of torture before execution of Indonesian Catholics (CathNews, 28/9/06)
Indonesia allows executed Catholic's body to return home (CathNews, 26/9/06)
Christians executed by firing squad (News.com.au, 22/9/06)
Public prosecutors reject Tibo et al's four last requests (Antara, 22/9/06)
Indonesia executes 3 Christians over Muslim deaths (Reuters India, 22/9/06)
Three Sulawesi militants executed (BBC News, 22/9/06)
Family of Tibo et al yet to be informed about execution (Antara, 21/09/06)
Indonesia: condemned men denied sacraments (Catholic World News, 21/9/06)
Execution looms again for Indonesian Catholics (CathNews, 20/9/06)
Demonstrators call for execution of Indonesian Catholics (CathNews, 5/9/06)
Fate of Bali bombers raises hope for three condemned Indonesian Catholics (CathNews, 22/8/06)
Miracle last hour stay of execution for death row Indonesians (CathNews, 14/8/06)
Thousands rally to save death row Catholics in Indonesia (CathNews, 11/8/06)
Indonesian Catholics to face firing squad on Saturday (CathNews 10/8/06) a/A>
Indonesian death row Catholics lose court appeal (CathNews 16/5/06)
Further appeal opportunity for Indonesian death row Catholics (CathNews 19/4/06)
Activists maintain fight for death row Indonesian Catholics (CathNews 10/4/06)
Second clemency plea for death row Indonesian Catholics (CathNews 28/3/06)
Pope sends envoy to death row Indonesians (CathNews 22/3/06)
Indonesian bishop condemns Catholics' death sentence (CathNews 29/11/05)
Looming execution of three Indonesian Catholics (CathNews 17/11/05)
Indonesian bishop concerned about resurgence of violence in Poso (CathNews 16/8/02)
4 Jan 2007