The Melbourne-based father-of-five, widely named as Islamic convert Adam Brookman, surrendered to Turkish officials earlier this week ahead of his arrival in Sydney late yesterday.
"A 39-year-old Australian national was arrested upon arrival at Sydney International Airport last night on an interstate arrest warrant, relating to his alleged involvement in the conflict in Syria," federal police said in a statement.
"The man voluntarily surrendered himself to Turkish officials in Turkey on Tuesday, July 21.
"His travel back to Australia was negotiated between the individual, the Australian Federal Police, Victoria Police, other Commonwealth government agencies and international partners."
No charges have yet been laid, although the Australian government has been vocal on insisting that anyone found to be engaged in terrorist activities would face the full force of the law.
Canberra's rhetoric has been stepped up in recent months as fears grow about the number of Australians fighting with jihadist groups and concern about the threat at home from radicalised individuals.
The government says some 120 Australians have left to fight in Iraq or Syria with 160 actively supporting extremist organisations at home through financing and recruitment.
Last month, the government introduced legislation into parliament to strip citizenship from dual nationals who help terrorists. It is not clear whether Brookman is a dual national.
Under Australian law, he would be guilty of a crime if he went to Syria with the intention of engaging in hostile activity, or to recruit other fighters.
Earlier this week, he claimed in an interview with Fairfax Media that he carried out humanitarian work in Syria and was forced to join the jihadist group after being injured and sent to IS-controlled territory.
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