Radical Indonesian cleric Abu Bakar Bashir has been charged with inciting people to commit terrorist acts.
The charges carry the death penalty.
The accusations relate to a militant training camp discovered in the province of Aceh in February.
Indonesian police say they believe Islamic radicals were planning assaults in the capital, Jakarta.
Lawyers for Abu Bakar Bashir say he denies the accusations.
The cleric served almost 26 months for conspiracy over attacks on Bali nightclubs in 2002 that killed 202 people, including three New Zealanders and 88 Australians.
He was cleared of involvement with Jemaah Islamiah, the group behind the attacks, and released in 2006.
The BBC reports the 71-year-old has been described as the spiritual leader of Jemaah Islamiah, which has links to al-Qaeda - a claim he denies.
He is now the leader of the hardline Islamist group Jemaah Ansharut Tauhid (JAT), which was created in 2008.