Abu Dujana - shot in the thigh during his arrest to stop him escaping - was seized by Indonesian crack anti-terror agencies, Detachment 88 and the Anti-Bomb Squad, on June 9 in Banyumas, central Java.
Anti-terror officers are now racing against time to glean as much information as they can from Dujana and his boss, Zarkasih, the leader of regional terror group Jemaah Islamiah (JI), to track down other militants, including Asia's most wanted terrorist, Malaysian Noordin Mohamed Top.
'Dujana is currently undergoing investigation and questioning,' an anti-terror source said.
'We hope to complete his dossier in two months' time and hand the case over to the attorney-general's office.'
The anti-terror sources say Dujana was involved in the 2003 J.W. Marriott hotel blast in Jakarta.
He is also accused of hiding Noordin and Malaysian Azahari bin Husin in 2003. 'Dujana met with Noordin shortly after the Marriott blast,' the source said.
Noordin and Azahari are both accused of masterminding Indonesia's major terrorist attacks, including the devastating Bali bombings in 2002, the Australian embassy car bombing in 2004 and the second Bali bombings in October 2005.
Azahari was killed by police in November 2005.