The suspect, Imam Samudra, is believed to be a senior member of Jemaah Islamiyah, the al Qaeda-linked regional terror group that has been blamed for the near-simultaneous bombings at two Bali nightclubs on Oct. 12.
Samudra, one of 33 people detained for the attack, was charged under the country's new anti-terror laws with planning the bombings. If convicted, he could face the death penalty, said Mohammed Salim, a spokesman for the prosecution.
Samudra, 33, was arrested Nov. 22 as he tried to flee Indonesia's main island of Java on a passenger ferry.
Police say Samudra learned bomb making in Afghanistan. He has admitted carrying out the bombings to reporters and has showed no remorse, saying the attack was to avenge the deaths of Muslims worldwide.
He was also charged with the bombings of four churches in Riau province in 2000 and the robbery of a jewelry shop, the proceeds of which were allegedly used to finance the Bali attack.
He is expected to face trial within 10 days, Salim said.
Prosecutors handed over several items of evidence to the court when they charged Samudra, including a laptop allegedly owned by him and a detonator used in one of the bombings.
Last week, Amrozi bin Nurhasyim became the first suspect to go on trial for the bombings. He allegedly bought the explosives and van used in the attack.
Jemaah Islamiyah is thought to be behind the Christmas Eve church bombings in Indonesia in 2000, as well as a foiled plot to blow up U.S., Australian, British and Israeli missions in Singapore.
The group's alleged leader, Abu Bakar Bashir, is currently on trial in Jakarta for treason in connection with the church attacks. He has not been charged in the Bali bombings.
The trials are seen as a test of Indonesia's willingness to crack down on radical Islamic groups in the world's largest Muslim nation.
They could also shed light on the inner workings of Jemaah Islamiyah, whose goal, according to regional law enforcement officials, is to establish an Islamic state across Southeast Asia.
Police and prosecutors say they have a strong case — including confessions from many of the suspects, testimony from dozens of witnesses and physical evidence, such as receipts for the explosives and the chassis of the minivan used in the attack.
Jemaah Islamiyah has been blamed for other bombings in Indonesia and thwarted attacks on the U.S. Embassy and other Western targets in Singapore.
Dozens of alleged Jemaah Islamiyah members have been arrested in Singapore and Malaysia.