Indonesian cleric Abu Bakar Ba'asyir led Islamic militant group Jemaah Islamiah, an Australian court heard.
Ba'asyir says he is a simple preacher
Jack Roche, on trial for attempted terrorism, said in evidence played to the court that he was a JI member between 1996 and 2000.
"Ultimately, he's the one who makes decisions," Mr Roche said of Ba'asyir.
The evidence comes as Indonesian prosecutors again try to link Ba'asyir with JI, after he was acquitted in 2003 of being its spiritual head.
Ba'asyir was released from jail in April after serving an 18-month sentence on immigration offences.
He was immediately re-arrested on suspicion of terrorism, and is being questioned over his links with JI, which is blamed for a string of bombings, including the 2002 Bali attacks.
Ba'asyir denies JI even exists.
Mr Roche is on trial for plotting to blow up Israel's embassy in the Australian capital Canberra.
He told police in interviews shown in court, and recorded in 2002, that he joined the Australian branch of JI in 1996.
At that time, he said, the spiritual leader of the group was a man called Abdullah Sungkar, but after he died, Ba'asyir took over.
Mr Roche admitted belonging to JI
"He's the one who makes decisions regarding the structure of JI in South East Asia," Mr Roche said of Ba'asyir.
Intelligence officials believe that the operations chief of the group was an Indonesian national called Hambali, who was detained by the US last year and is being held in a secret location.
Mr Roche told federal police that he believed Hambali was lower than Ba'asyir in the JI hierarchy.
"I believe he was under Abu Bakar Ba'asyir," he said in excerpts of a taped interrogation played in court.
'Break with JI'
Mr Roche said he left JI in mid-2000, around the time prosecutors allege he was plotting to bomb the Israeli embassy.
He said that he fell out with the twin brothers who are alleged to have headed Australia's JI, Abdul Rahim Ayub and Abdul Rahman Ayub.
"We didn't see eye to eye on certain issues and I didn't see that there was any benefit for me in continuing my association with them," Mr Roche said on the tape.
Last week, prosecutors told the court that Mr Roche also discussed a possible attack on the 2000 Sydney Olympics.
The plot was later overruled by members of Osama Bin Laden's al-Qaeda network when Mr Roche travelled to Afghanistan, according to his notes.
Prosecutors said Hambali paid Mr Roche US$80,000 to carry out the embassy bombing.
Mr Roche's lawyer has insisted his client is innocent and rejects violence.
He faces a maximum sentence of 45 years in prison if convicted.
The English-born suspect converted to Islam more than a decade ago and has been living in Perth in Western Australia for several years.
The trial continues.