The control order will restrict the movements of Jack Thomas, 33, who was forced to cut short a post-prison beach holiday with his family to return to his home in Melbourne.
Attorney-General Philip Ruddock said the interim order was about "protecting the Australian community, not punishing the person for an offence".
Under the order Mr Thomas has to stay in his Melbourne home from midnight until 5:00 am daily and report to police three times a week, Mr Ruddock told a news conference.
Earlier this month the Victoria Court of Appeal overturned Mr Thomas's conviction and sentence of five years in jail for receiving money and an air ticket from Osama Bin Laden's al-Qaeda.
The court ruled that an interview carried out by Australian police while he was in custody in Pakistan, which formed a major part of the state case, was inadmissible.
His lawyer, Rob Stary, said Mr Thomas would "vigorously challenge" the control order, which was served while he was holidaying at the beach with his wife and children.
"He was slapped with a court order and told to get back to Melbourne immediately," his brother Les told reporters.
"Anyone who cares about civil liberties should be outraged at this decision," he said, accusing the authorities of persecution.
A control order can be granted if it is thought it might prevent a terrorist attack, or if it is suspected a person has received training from a terrorist organisation.
Mr Thomas was the first person jailed under anti-terrorism funding laws adopted in October 2002 in the wake of the September 11 attacks and a bombing linked to al-Qaeda which killed 202 people -- 88 of them Australian -- in the Indonesian resort of Bali.
Prosecutors alleged Mr Thomas trained at al-Qaeda bases in Afghanistan before the group launched its September 11, 2001 attacks on the United States and then stayed in safe houses frequented by al-Qaeda operatives after moving to Pakistan in 2002.
The former Melbourne taxi driver was convicted of accepting US$3,500 in cash and an air ticket home from a senior al-Qaeda operative in Pakistan.
Mr Thomas said he accepted the money and plane ticket simply because he wanted to return home to his family and had no intention of becoming an al-Qaeda operative.