Australian ISIL orphans rescued from Syria camp
The children and grandchildren of two notorious jihadis are now in the care of Australian officials, he said in a statement.
The children are believed to be aged between two and 17 and were living in a camp in northern Syria -- making consular access all but impossible.
Morrison previously indicated his government would only help citizens if they approached an embassy or consulate but appeared to have had a change of heart.
"The fact that parents put their children into harm's way by taking them into a war zone was a despicable act," Morrison said in a statement.
"However, children should not be punished for the crimes of their parents."
The group includes three surviving children and two grandchildren of Sydney-born Khaled Sharrouf -- who came to prominence after posting a photo of one of his sons holding the head of a Syrian soldier.
There are also three children of Yasin Rizvic who travelled from Australia to Syria with his wife.
Both ISIL fighters are presumed dead.
Morrison did not name the children or elaborate on how they were removed, but confirmed they were "repatriated from the conflict zone into the care of Australian government officials".
The Australian Broadcasting Corporation reported that the children had been moved to a country neighbouring Syria.
Their case had gained widespread attention after the grandmother of the Sharrouf children -- 17-year-old heavily pregnant Zaynab, her younger sister Hoda, their eight-year-old brother Hamzeh, and Zaynab's two young children Ayesha, three, and Fatima, two -- had pleaded with Canberra to bring them home.
Grandmother Karen Nettleton even travelled to the camp earlier this year to meet them but was rebuffed by authorities, and Morrison said he did not want to put Australian lives at risk.
The prime minister on June 24 repeated his concerns, adding that "repatriating these children was not a decision the Australian government made lightly".
"Australia's national security and the safety of our people and personnel have always been our most important considerations in this matter," he said.
The fate of foreign fighters and their families has become a significant problem for governments as the conflict against ISIL draws to a close.
Several European countries, including France and Belgium, have repatriated children from Syria in recent months.