His comments came after news emerged that the wife of one Australian Islamic State (IS) militant wanted to return home with their children.
But Mr Dutton said such decisions would be made on a case-by-case basis.
Proposals announced on Tuesday could see some Australians lose citizenship for supporting terror groups.
Local media have reported that the wife and children of Australian IS fighter Khaled Sharrouf are trying to return to Australia.
The family of Sharrouf's wife, Tara Nettleton, is trying to help her and the couple's five children return to Sydney, Fairfax Media reported on Wednesday.
Among them is a young son believed to be the boy photographed last year holding the severed head of a Syrian.
Asked on Wednesday about news of their return, Mr Dutton said the childrens' mother, Tara Nettleton, could also be charged with terrorist offences.
He said the treatment of the children of returning suspects would depend on the circumstances and the ages of the children.
"If they're infants, for example, then they would be in state care, as we've seen with some people who have decided to abandon their children and go off and fight," he said.
"So those arrangements would operate as they would with any family where parents have abandoned their children or not acting in the best interests of their children."
Sharrouf was jailed in 2009 for four years for being part of a cell planning attacks in Sydney and Melbourne.
After his release he was banned from leaving the country but used his brother's passport to travel to Syria with his family.
Ms Nettleton's father, Peter Nettleton, told local media on Wednesday that he had not seen his daughter for 10 years and had only met two of his five grandchildren.
"I still love my daughter and I hope she comes home safely," Mr Nettleton said in a brief statement made from outside of his home in southern Sydney.
Ms Nettleton's mother, Karen, is reportedly trying to help her daughter and grandchildren return to Australia.
According to the government, at least 100 Australians are fighting with terror groups in the Middle East, and as many as half of them have dual citizenship.
Another 150 people in Australia are known to be supporting such groups, while Australia's intelligence agency, the Australian Security Intelligence Organisation (ASIO), is investigating about 400 high-priority terrorist cases.
Australians fighting overseas with terror groups could have their children removed from their care, Immigration Minister Peter Dutton has said.