Fabianus Tibo, 60, Dominggus da Silva, 42, and Marinus Riwu, 48, of the island of Sulawesi, were arrested in 2000, accused of homicides and sectarian violence in Poso, in Central Sulawesi province.
They were sentenced to death by the regional court of Palu in 2001 for a massacre of Muslims.
The Rome-based Community of Sant'Egidio recently launched an appeal to save the three Indonesian Catholics.
The ecclesial movement in a communiqué said that the three, "illiterate and poor, are probably only scapegoats, given that, following the discovery of new proofs it is uncertain that they were the material executors of the crimes, while the masterminds of the bloody disturbances of Poso continue to be unknown."
Numerous organizations at the national and international level, including representatives of the Muslim community, have expressed their support for "Tibo and companions," as the three are now known. Their trial was marked by pressure from Muslim extremists.
Last March 19, Bishop Joseph Theodorus Suwatan of Manado visited the three condemned men as Benedict XVI's "special envoy."
The AsiaNews agency warned that the Supreme Court has rejected the second appeal of the three men's sentence.
Today, Chief Supreme Court Justice Bagir Manan said that legal proceedings are over and that the legal route was closed for the legal team set up by the Advocacy Service of Justice and Peace in Indonesia (PADMA).
"PADMA's efforts are against the law," Manan added. "The death sentence is final and the fate of the three convicts is no longer in our hands."
On Wednesday, Attorney General Abdul Rahman Saleh said the three Catholics will be executed "possibly in April."
On April 1, the Office of the State Attorney General announced a delay of the execution, because "important papers" were missing.
Four days later, the attorney told the press that the legal review of the case by the PADMA group of lawyers, and the moral support of human rights activists and religious leaders, will not serve to change the verdict.
Leaders of religious communities of Central Sulawesi fear that the execution of the three Catholics would spark new interreligious confrontations in the area.