His trial comes after the conviction last year of JI co-founder and the spiritual leader of the jihadist movement in Indonesia, Abu Bakar Bashir, following the discovery of a secret paramilitary training camp in Aceh.
Bashir served almost 26 months behind bars for conspiracy over the 2002 Bali bombings but that conviction was later overturned.
Like Bashir's trial, the case against Patek will be conducted amid heavy security, with authorities on high alert for the possibility of reprisal attacks.
Patek also faces murder charges over his alleged role in a series of bombings of churches in Indonesia in 2000 that killed 18 people.
The murder charges in relation to Bali and the 2000 attacks carry a maximum penalty of death, and a minimum of 20 years in prison.
He will also face charges of conspiracy to commit terrorism, harbouring information on terrorism, possession of explosives and firearms, and two counts of document fraud.
The trial is expected to run until late May or early June.