Hambali allegedly headed JI until late 2002. He was arrested in Thailand in August 2003 and handed over to US authorities.
He appeared before a Combatant Status Review Tribunal, an administrative hearing, at Guantanamo Bay on April 4, as one of 14 "high value" detainees transferred to the base in September after being held at secret CIA prisons abroad.
The Bali blasts claimed 202 lives,
most of them foreigners [AP]
The public and reporters are not permitted access to the hearings.
A US government transcript of the unclassified portion of Hambali's hearing was released by the Pentagon on Thursday.
"Mr Hambali, did you have any association with al-Qaeda while you were a member of JI?" the judge of the military commission charged with determining his status as an "enemy combatant" asked.
Hambali was quoted as replying via an interpreter: "No."
According to the summary of evidence released by the Pentagon: "The detainee was the operations chief of the Jemaah Islamiyah and its main contact and point man for al-Qaeda in South-East Asia."
The Pentagon also released the transcript of a closed hearing for Ali al-Azia Ali, also known as Ammar al-Baluchi, who is accused by US authorities of helping arrange financing for at least one of the September 11 hijackers.
Ali said he is an ordinary businessman who has family ties to Khalid Sheikh Mohammed, the man named as the mastermind of the 9/11 attacks, but is not part of al-Qaeda.