According to the ABC, an eight-year-old boy was forced to leave Turkey with his family after they were arrested in an IS safehouse in Istanbul on January 16.
It's believed the family - along with their Indonesian father - is now being held in Jakarta by counter-terror officers.
The family was reportedly arrested on arrival in Denpasar, Bali, on Saturday.
The ABC reports the boy was born in South Australia in 2009 while his father was studying there.
Indonesian police say the couple travelled to Turkey via Malaysia with their three children because the 39-year-old father, who has been named as Triono, wanted to be an IS fighter.
Australia sought an extradition deal with Turkey in 2015 for the capture and return of potential Australian foreign fighters.
