The Australian Security Intelligence Organisation estimates about 100 Australians who left to support or fight for IS remained in Syria or Iraq.
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ASIO boss Duncan Lewis told a Senate estimates hearing on Tuesday that it was unclear how they would react to the imminent defeat of the terror-network in the war-torn region.
"With the military and territorial demise of ISIL which has resulted in the dispersal of foreign fighters including Australians, there is less certainty about what to expect in terms of their return," he said.
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However, Mr Lewis said he did not expect a large scale influx of Australians with terror connections.
"We're working hard to ensure they're managed and dealt with appropriately."
His comments follow the highly-publicised case of a teenager who left the UK to join IS in 2015 and is now pleading to return home with her newborn baby.
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The future of , 19, has stirred much controversy in London with some concerned about her innocent baby and others arguing she poses a danger to society and should be refused re-entry.
The US-led Arab and Kurdish forces are close to capturing the so-called IS "caliphate's" last territorial holdout in Syria.
US President Donald Trump has demanded that other countries take back hundreds of captured IS fighters.
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Trump said on Twitter that the United States was asking Britain and other continental allies "to take back over 800 ISIS fighters that we captured in Syria and put them on trial".
In April 2018, a Sydney man who travelled to Syria in 2013 with the intention of fighting in the war-torn region was jailed for at least two and a half years.
He was arrested in 2016, more than two years after returning to Australia.
