Opening the case in a central Jakarta court on Wednesday, prosecutors said Dujana had authorised the shipment in 2006 of two caches of explosives for attacks against Christians and government workers in the town of Poso in eastern Indonesia.
Poso has been the scene of a series of attacks in recent years by Muslim fighters against Christians and government workers.
In addition, Dujuna was also charged with harbouring and assisting Noordin Top and Azahari Husin, two Malaysians high on Indonesia's wanted list for several deadly attacks in recent years.
Azahari was killed in a police raid two years ago while Noordin is still on the run.
The CIA and other Western intelligence agencies have said previously that JI has close ties to Osama bin Laden's al-Qaeda network.
In a video shown by Indonesian police shortly after his June arrest Dujana said he had undergone guerilla training in the Pakistani city of Peshawar and in Afghanistan.
Before the start of his trial on Wednesday, Dujana said JI's goal of "defending the Muslim people and Islam" had not changed.
"There are other people outside jail running the operation," he told The Associated Press from a holding cell at the South Jakarta District Court.
"It is up to them to decide if they want to continue or not."
JI has been blamed for a series of deadly attacks in Indonesia including the Bali bombings in 2002 that killed 202 people.
The group was also allegedly involved in the 2003 and 2004 attacks on the JW Marriott Hotel and the Australian Embassy in Jakarta, as well as the 2005 triple suicide bombings on restaurants in Bali.
Following the reading of the charges in court on Wednesday the trial was adjourned until next week when the defence will respond.