Prime Minister Scott Morrison on Monday said that the decision to repatriate the group of eight children was not made "lightly", reports Xinhua news agency.
"Australia's national security and the safety of our people and personnel have always been our most important considerations in this matter," he said in a statement.
"As I have said repeatedly, my government would not allow any Australian to be put at risk.
"The fact that parents put their children into harm's way by taking them into a war zone was a despicable act.
"However, children should not be punished for the crimes of their parents."
The group includes three children and two grandchildren of well-known Australian radicals Khaled Sharrouf and Tara Nettleton, who in 2014 released images on social media of one of his children holding a decapitated head, reports Efe news.
Nettleton died of health complications in the Iraqi city of Mosul in 2015 and Sharrouf was killed in an airstrike near Raqqa, Syria, in 2017, along with the couple's two eldest children, Abdullah and Zarqawi.
It is not known where the evacuees were taken, including Sharrouf and Nettleton's eldest daughter Zaynab, aged 18, who was reportedly rescued with her two sons and may have given birth to a third.
According to the government, up to 70 Austral are in refugee camps in Syria, the vast majority of whom are children or women.
( With inputs from IANS )