Mohammad Isa was captured in North Sumatra in April with ten other illegal immigrants from Afghanistan and has since been held in the Australian-built Tanjun Pinang immigration detention centre on Bintang Island, The Australian newspaper reports.
He is said to be a medical doctor who speaks eight languages.
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The head of Indonesia's international crimes unit, Saud Usman Nasution said the arrest marked the first time an asylum seeker had been linked to potential terrorism.
He had previously indicated a suspected asylum seeker was linked to al-Qaeda but this is the first time the man's identity has been confirmed, The Australian says.
The provincial head of immigration in North Sumatra, Sahala Pasaribu told The Australian he had processed the man after his arrest in April.
"We learned from (Indonesia's specialist anti-terrorist police squad) that at least one mobile phone held by this group of 11 Afghans had been used to contact senior al-Qaeda figures," he said.
General Nasution has warned that some asylum seekers trying to reach Australia via Indonesia could have terrorist backgrounds.
