Imam Samudra, Amrozi Nurhasyim and Ali Ghufron have "exhausted their legal options," Attorney General spokesman Jasman Panjaitan told reporters Friday.
The men were sentenced to death in 2003 for planning and helping to carry out the Oct. 12, 2002, suicide bombings targeting two nightclubs on the resort island of Bali that left 202 people dead, 88 of them Australian tourists and 38 Indonesian citizens. The bombings also crippled Bali's tourism industry.
The executions will be carried out by firing squad on the island of Nusakambangan, where the three men are being held in a maximum security prison, officials said.
The men were part of Jemaah Islamiyah, a Southeast Asian militant group blamed for at least three other suicide bombings in Indonesia. The 2002 bombings were allegedly funded by al-Qaida.
Amrozi, Mukhlas and Samudra have refused to seek clemency from Indonesian President Susilo Bambang Yudhoyono after the Supreme Court rejected their final appeals, saying they want to die as martyrs.
In an earlier statement from their lawyers, the condemned men said their blood would "become the light for the faithful ones and burning hell fire for the infidels and hypocrites."
In an interview with Reuters late last year, the militants said they regretted only that some Muslims were killed in the blasts.
Brought before the media at the island prison in southern Java earlier this month, they vowed their deaths would be avenged.
"If I'm executed there'll be retribution. It's not necessary for me to tell you what the retribution will be," said Amrozi, known as the "smiling assassin" for his jovial courtroom behavior.
Supporters of Jemaah Islamiyah are expected to gather in the thousands after the execution to mark the passage of their comrades' bodies back home for burial.
Security forces told the BBC they are considering flying the bodies back rather than allowing the crowd a long and emotional trip by road.
The Australian government on Friday advised its citizens to reconsider the need to travel to Indonesia, including the popular resort island, citing the "very high" threat of attacks.
Although there have been no major bomb attacks since 2005, Indonesia is still considered at risk. In his annual address to parliament on August 15, President Yudhoyono warned that the "country is still unsafe from terrorist acts."
Police are still seeking Noordin Top, a Malaysian considered a key figure behind a series of bombings, including a second set of blasts in Bali in 2005 that killed more than 20 people.