Seven other suspects had their trials postponed for procedural reasons.
Totok Bambang, a prosecutor, told the court that the men "plotted or attempted terrorism, spreading fear or causing mass casualties".
"What I was trying to do was defend Islam and Muslims"
Mohammad Hasan Saynudin, terror suspect
The suspects could be jailed for life or face the death sentence if convicted on the different charges.
The suspects were arrested last July after Indonesian anti-terrorism police found 20 bombs in a house in Palembang, which is about 425km from Jakarta, and in other parts of south Sumatra.
They allegedly planned to attack a bar frequented by non-Muslims in a resort town on the island of Sumatra with 22 explosive devices packed with bullets, but later called off the attack to avoid Muslim casualties.
Prosecutors also accused them of fatally shooting an Indonesian Christian teacher in 2007 and trying to kill two Catholic priests in 2005.
Mohammad Hasan, a former English teacher, told the court on Tuesday that he stood by his actions unless they were not "in accordance with the Quran and the prophet's guidance", otherwise, "I don't regret even a bit".
Prosecutors say he had acted as a courier between Osama bin Laden, the al-Qaeda leader, and Hambali, a senior JI operative in South-East Asia, before the September 11, 2001 attacks in the US.
The Jemaah Islamiyah group has been accused of five suicide bombings against targets in Indonesia in the past six years - including the 2002 Bali attacks - that killed more than 240 people.
Indonesia has convicted scores of terrorism suspects in its fight against terrorism, including executing three men last year for their role in the Bali bombings.