The government-hosted talks brought together 124 people convicted of terror-related crimes and some 51 survivors or family members of those killed in attacks.
But it drew fewer than expected survivors as two victim's rights groups shunned the event, saying the face-to-face meeting in the ballroom of a Jakarta hotel was poorly planned.
"There are so many of them (former convicts) in the room. We're not ready psychologically," said Ni Luh Erniati, an adviser to the Indonesian Survivors Foundation, which did not attend.
"We have forgiven them but we cannot predict what would happen if our emotions were ignited."
Indonesia, which has the world's biggest Muslim population, has suffered a string of extremist attacks this century, including the 2002 Bali bombings that killed more than 200 people.
Most of the dead were foreign tourists but 38 Indonesians were among those killed.
Erniati lost her husband in the Bali attack and later founded the Isana Dewata Foundation to represent families of those killed.
Both the Isana Dewata and Indonesian Survivors foundations stayed away from Wednesday's event.
"We've tried similar smaller-scale events in the past but it was hard even then," said Erniati. "Some survivors were so emotional and they became furious at the former militants."
But some victims were able to dispel their anger and attend the talks.
"If I succumb to my resentment, I would not be any different from them," said Febby Firmansyah -- badly injured in Jakarta's 2003 JW Marriott hotel bombing that killed twelve.
He refused to hold a grudge despite a mangled hand and permanent burn scars all over his body.
"I cannot force other survivors to forgive them as quickly as I did... so I warned them: don't come if you are not ready," he told AFP at the meeting.
'I am sorry'
Sumarno, who served four years in jail for delivering and helping pack explosives used in the Bali bombing, said terror attacks must stop.
"It's hard and saddens me to see survivors who are now suffering from permanent disabilities," said the former militant, who like many Indonesians goes by one name.
"I had not imagined the impact would be like that. I am sorry and have apologised to them."
He added that the meeting might help soften "discrimination" toward convicted militants who can have trouble finding work and fitting back into society.
Wednesday's meeting was the last of a three-day event which included remarks from government ministers along with education, social affairs and religious officials.
Only the convicted militants took part in classes about tolerance and diversity held earlier in the week.
Some cast doubt on the meeting when it was first announced last month, while there was also suspicion that it chief purpose was to boost the power of Indonesia's counter-terrorism agency by bringing the oversight of terror victims under its authority.
Chief Security Minister Wiranto rejected those claims Wednesday.
"This event is unprecedented. It's never happened before," he said.
"This event goes beyond just being ceremonial."
Jakarta has been running a deradicalisation programme for a number of years while a crackdown has weakened the most dangerous terror networks.
But fears have grown of a resurgence in militancy after hundreds of Indonesians flocked to the Middle East and the Philippines in recent years to join the Islamic State group or its allies.
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