Riduan Isamuddin, known as Hambali, was arrested by Thai and US authorities in Thailand in mid-August.
He is being questioned at the US-British air base on Britain's remote Indian Ocean island Diego Garcia, Time magazine reported, citing a regional intelligence official.
According to copies of his confession obtained by Time, Hambali said al-Qaida sent him $30,000 to pay for the bombing of two nightclubs in Bali, an idyllic island which is largely Hindu.
“Al-Qaida was highly satisfied with the Bali bombing and as a result provided additional money” totalling $100,000, an interrogation report said, AFP reported.
Some $45,000 was distributed to Jemaah Islamiyah, a group seeking the creation of a Muslim pan-Asian state, in Indonesia, Hambali said.
“Al-Qaida was highly satisfied with the Bali bombing and as a result provided additional money”
A interrogation report cited Hambali as saying
A further $15,000 dollars was to support the families of the imprisoned Bali bombers, and $30,000 was to finance new attacks.
Hambali said a portion of the money could have been used for the bombing of the Marriott Hotel in Jakarta in August, which killed 12 people, Time reported.
Other targets considered for attack included US and British embassies in Bangkok, nightclubs in Thailand, and shopping centres popular with western expatriates in Manila's elite Makati district.
“The prisoner mentioned that Jewish targets were always the main priority,” according to a report about Hambali obtained by Time, which said he had scouted the Israeli embassy and a synagogue in Manila.
Hambali and Lillie both described links between al-Qaida, Jemaah Islamiyah and the Philippines' Moro Islamic Liberation Front, saying $27,000 had been transferred this summer to the group, according to Time.