Police say Indonesian Bahrun Naim working for ISIL funded deadly attack that killed two civilians and five attackers.
A US military court has charged an Indonesian detainee at Guantanamo Bay in connection with a 2002 bombing in Bali, according to documents obtained by the Associated Press news agency.
The detainee, known as Hambali, was also charged in connection with an attack on the JW Marriott Hotel in Jakarta in 2003.
According to rules of the US military commission, a military court will later decide whether a trial will be held.
The October 12, 2002, Bali resort island attacks, which occurred near the US consulate, killed 202 people.
A suicide bomber blew himself up inside a nightclub jammed with tourists at a popular beach, killing many instantly and forcing others to run outside.
Another suicide bomber detonated a massive bomb loaded into a car parked on the street in front of two clubs.
In the second bombing, which occurred on August 5, 2003, the JW Marriott Hotel in Jakarta was targeted because the building was susceptible to the type of bomb that was being constructed.
The perpetrators believed there would be a large American presence at the hotel and they “believed it would have the biggest overall impact”, the charging documents said.
The August 5, 2003, car bomb in front of the hotel in Jakarta killed 12 people and wounded 150.
Last fall, a US government review board rejected the release of Hambali, saying he continues to be a “significant threat to the security of the United States”.
Hambali, whose real name is Encep Nurjaman, appeared before the board in August by video link, seeking his release after being held 10 years at the base without charge.
The Pentagon described him in a profile released before the hearing as a leader of the Southeast Asia-based Jemaah Islamiyah armed group. Hambali also is alleged to have had links to al-Qaeda.
Hambali has been charged with murder and attempted murder in violation of the law of war; intentionally causing serious bodily injury; “terrorism”; attacking civilians; and related charges.
Australia on Saturday welcomed the reported US charges against Hambali.
“I hope that should this prosecution succeed, it will bring closure to those devastated by the loss of loved ones, family and friends,” Julie Bishop, Australia’s foreign minister, said.
“It has been a scar on the hearts of all Australians since these attacks occurred in 2002.”
For Australia, which suffered the most casualties, the Bali bombs were the worst peacetime attack on its citizens.
Seven Americans and 38 Indonesians citizens were also among the dead.
Bishop said Australia would provide whatever support it could, but did not support the death penalty.
“Those responsible for the murder of 202 people, including 88 Australians, should be prosecuted, should receive the severest of punishment and should never be freed,” she said.