"The pain generated by a firing squad is a natural effect, and it's not torture," court chairman Mohammad Mahfud MD told reporters.
The case was presented to Indonesia's constitutional court when the three men were about to be executed shortly before the Muslim fasting month of Ramadan.
"The pain generated by a firing squad is a natural effect, and it's not torture"
Mohammad Mahfud MD,
During the hearing witnesses who had seen other executions testified that in one case someone was still alive up to seven minutes after being shot and was obviously in deep pain.
The bombers also said that according to Islamic law beheading would be the right method of execution.
Another more "humane" method would be a lethal injection, they argued.
More than 200 people died in the Bali nightclub bombings, many of them foreign tourists.
As a result the case and the fate of the bombers has attracted intense international interest.
Indonesia's attorney general has said he will give more details about the time of execution this coming Friday, with analysts saying the execution could follow within days.
The executions, considered a politically highly sensitive issue in Indonesia, have been delayed on several occasions without clear reasons.
Indonesian police are reported to have planned a massive security operation to handle any violence that follows the executions.
Most executions in Indonesia are carried out by firing squad at undisclosed locations late at night.