"It has been submitted to the south Jakarta court today," Didik Istiyanta, south Jakarta state prosecutor, said on Friday.
Asked whether the charges related to terrorism, he said, "Something like that," adding, "but for details, wait until the trial".
Another prosecutor, Andi Herman, confirmed the charges were related to terrorism. "Yes, they are," he said, but declined to elaborate.
Herman said normally a trial would be convened within two weeks of the charges being submitted.
The attorney general's office had said earlier Bashir would face charges of helping to plot the August 2003 blast at the JW Marriott hotel in Jakarta which killed 12 people and of involvement in a conspiracy to hide large amounts of explosives in central Java.
Authorities believe Bashir inspired fighters who bombed nightclubs on the tourist island of Bali in 2002 and who carried out the Marriott bombing and other attacks.
Bashir, who denies any connections with Jemaah Islamiya or terrorism, was first arrested days after the Bali blasts that killed 202 people, amid suspicions he led Jemaah Islamiya and had links to violent acts.
The JW Marriott hotel bombing in
Jakarta killed 12 people last year
However, following a trial using the ordinary criminal code, the court said there was not enough evidence to prove Bashir led the group, and ultimately only convictions related to immigration violations were upheld in appeals courts.
After he had served time on those convictions, Indonesian police detained Bashir under a tough anti-terror law passed
in the wake of the Bali bombings.