Four women and nine children who had links to the terrorist organisation will return to Australia on Thursday, arriving in Sydney and Melbourne after years spent in a Syrian refugee camp.
Some of the women face the prospect of being arrested on arrival by police upon landing.
Education Minister Jason Clare said reintegration into society of the children would be difficult, but options would be there for children if their mothers were arrested.
"I would expect that they would be cared for by other members of their family," he told ABC TV on Thursday.
"Kids don't get to choose who their parents are, and these children have seen sorts of things that no child should ever be exposed to, and it's going to take time for these children to reintegrate into Australian society.
"I would expect that the federal police would want to run counter-extremism programs with all of the children that return."
The group of women and children are all Australian citizens, with the federal government saying there were limits to measures stopping their return.
Mr Clare said federal police would be monitoring the cohort closely upon their return.
"I've got faith in the Australian police. They know what they're doing. This is not their first rodeo," he said.
While some women travelled willingly to support their partners who wanted to fight for Islamic State, advocates for the group say others were trafficked, or only went to the Middle East to keep their family together.
All children in the group of 13 returning home would likely need help integrating into Australian society after years in Syrian camps, while others could need more intensive deradicalisation support, leading extremism researcher Michele Grossman told AAP.
"This is going to be very much case by case," the Deakin University professor said.
"We can't make assumptions that all children will respond equally ... to the kinds of indoctrination activities that we know have gone on in those camps."
Prof Grossman said support from the community would be crucial to help them recover from years of trauma.
"Communities have to be willing - with appropriate support, with appropriate knowledge and transparency - to be part of the picture," she said.
"If the community is only ever going to turn them away and refuse to have anything to do with them ... then what hope are you giving them, and what prospects are you offering them?"
One woman has been barred from entering Australia on national security grounds and the opposition has reiterated its calls for the entire group to be blocked.
Greens leader Larissa Waters said while charges should be laid for any offences, there were concerns for how they were being treated.
"I'm pleased that these kids and their mums are returning home. They're Australian citizens," she told ABC Radio.
"These kids and women are being used as a political football, and I would like to see our government stand up for the rights of our citizens and help these folk reintegrate."
While each child would be different, many of them would have little memory of what Australia was like, violent extremism specialist Peta Lowe told AAP.
Previously director of countering violent extremism in NSW Youth Justice, Ms Lowe said some of the children might have more complex needs but others could only need a safe environment to reintegrate.
"It may not be any conversations at all about religion or political beliefs," she said.
"It may be around those very normal things that we would do for children when they've come out of risky situations."
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