Thousands of protesters took to the streets of eastern Indonesia after three Christian militants were executed in religiously divided Sulawesi.
Thousands of mourners are praying for the dead men
Protesters torched cars, looted shops and set prisoners free from a jail.
But Palu, where the executions took place, remained calm. Mourners attended church services to pray for the men.
The three men were convicted of masterminding a series of attacks on Muslims in central Sulawesi in 2000 that killed at least 70 people.
A spokesman for the Vatican, which had appealed for clemency, described the executions as a defeat for humanity.
Previously known as Celebes, Sulawesi is Indonesia's fourth largest island
80% of residents are Muslim, while 17% are Christian
A December 1998 brawl in Poso led to months of religious violence in which hundreds died
The human rights organisation Amnesty International also expressed disappointment.
The three men - Fabianus Tibo, Marianus Riwu and Dominggus da Silva - were taken before the firing squad before dawn on Friday morning, according to police officers.
The bodies of Tibo and Riwu were then flown to their home towns, while Da Silva was buried in Palu, the provincial capital.
The attacks the three men were accused of instigating, in Poso, was part of a wave of violence triggered by a brawl between Christian and Muslim gangs in December 1998.
The violence left more than 1,000 people dead. The two sides signed a peace deal in 2002, but there have been sporadic incidents since.
As news of the execution emerged, at least 1,000 mourners packed the main Catholic church in Palu to pray for the three men.
Rioting broke out elsewhere, including on the island of Flores, the men's birthplace, and in Tibo and Riwu's Sulawesi villages as well as in Poso.
The worst violence broke out in the Christian-dominated town of Atambua in West Timor, where Da Silva was from.
At least 1,000 people took to the streets, throwing stones and looting shops.
Rioters damaged the state prosecutor's office and broke into the jail, freeing some 200 inmates. Only 20 prisoners had so far returned, police said.
One Catholic priest in Atambua told the AFP news agency he and three colleagues had managed to placate the rioters and they were now heading home.
National deputy police chief Adang Daradjatun stressed that the violence was being directed at the authorities, not at Muslims, and Indonesia was not witnessing a resurgence of the religious conflict of six years ago.
The case against the men has raised questions in Indonesia about the different sentences handed down to Christians and Muslims.
Few Muslims were ever punished for the violence in Sulawesi, and none to more than 15 years in jail.
The executions have highlighted the religious divide
Human rights workers also claim that while it was possible the three men took part in some of the violence in 2000, they were almost certainly not the masterminds.
The executions had been due to take place last month, but the three men were given a reprieve after a plea for clemency from Pope Benedict XVI, and demonstrations by thousands of Christians.
Despite government denials, many Indonesians connect the timing of the men's deaths with the planned execution of three Muslim militants for their part in the 2002 Bali nightclub bombings, that killed more than 200 people.
These men were also given a reprieve last month, and are now filing final appeals for clemency.
Indonesia is home to the world's largest number of Muslims. But in various eastern areas of the country, such as parts of Sulawesi, Christian and Muslim populations are roughly equal.