"The case was a pure enforcement of law. It has nothing to do with the questions of tolerance between Islam and other religions," Hassan Wirajuda, the country’s foreign minister told The Associated Press on the sidelines of the UN General Assembly meeting in New York.
"All the legal remedies have been exhausted," he said.
The foreign minister’s remarks came on Sunday when thousands of mourners packed churches in Christian-majority parts of Indonesia to pray for the executed men.
Soldiers and police - fearful of renewed violence - tightly guarded churches and mosques in Poso and along roads leading to Beteleme, where two of the three militants were to be buried.
Fabianus Tibo, 60, Marinus Riwu, 48, and Dominggus da Silva, 42, were convicted of leading a Christian militia that carried out a series of attacks in May 2000, including a machete and gun assault on an Islamic school where dozens of men were seeking shelter.
But human rights groups said the trial was a sham, while others said the government's decision to execute the men raised questions about the role religion played in doling out punishment for four years of bloodshed.
Only a handful of Muslims were convicted, all to 15 years in jail or less.
The Vatican expressed "great regret" over the executions, and called for reconciliation and peaceful coexistence among different religions in the country. The uproar occurred as many Muslim around the world protested recent comments about Islam made by Pope Benedict XVI, who has since expressed regret.
Wirajuda said the cases were reviewed by local courts, provincial courts and the Supreme Court. The government, he said, must now meet with religious leaders to convince them that justice had been carried out without consideration of religion.
"We have a truly independent judiciary," Wirajuda said. "This is a new Indonesia."
Thousands of Muslims rallied in the weeks leading up the executions demanding that the men be killed. The executions were already delayed twice, most recently last month following an appeal by the pope.
Many said on Sunday that they were satisfied that justice had finally been carried out.
Sugiarti, a 40-year-old Muslim woman who lost her husband and three children in the May 2000 violence, said the Roman Catholic militants "deserved to die for what they did to my family and our community."
The funeral of Tibo and Riwu on Sunday coincided with the first day of the Islamic holy month of Ramadan in the world's most populous Muslim country.