The so-called "ISIS brides" travelled from a refugee camp in northern Syria for families of killed or detained Islamic State militants.
The first group of two women and their children touched down in Melbourne shortly after 4.30pm on Tuesday, having flown with Qatar Airways via Doha.
A group of four women and their children arrived at Sydney airport, where they were taken out a back entrance, avoiding waiting media.
Members of the Victoria and NSW Joint Counter Terrorism teams awaited the groups.
"The cohort was subject to a range of operational responses, including the searching of belongings and the downloading of their devices for investigative purposes," NSW and Victoria police said in a statement.
"No-one arriving within this cohort has been charged, however, investigations into the activities of Australians who travelled to Syria – including those who have since returned – are ongoing."
A sizeable media pack awaited the Melbourne group's arrival, in a similar scene to that awaiting the previous cohort of women and children earlier in May.
Three men dressed in black were gathered at the arrivals gate, fewer than the dozens who waited for the last group.
A second, larger group of four women and their children landed in Sydney about an hour later, where uniformed police were out in greater numbers.
They will have access to assistance from the Department of Communities and Justice, as has been the case with past repatriations.
"NSW has arrangements in place to work with the Commonwealth to safely manage and support families should they return from camps in Syria," a department spokesperson told AAP.
They will have access to medical, mental health and education services as well as supports related to their experiences at the refugee camp, they said.
The group originally travelled to the Middle East with men who sought to fight for Islamic State before the caliphate was toppled in 2019.
The Australian government has spent more than a decade preparing for their return from the al-Roj refugee camp in northern Syria.
Speculation mounted about whether any of the women would face arrest after three Islamic State-linked women were charged upon their return to Australia earlier in May.
They were among a cohort of four women and nine children who flew into Sydney and Melbourne after leaving the same refugee camp.
Two are facing charges relating to slavery, and a third was charged with joining a terrorist organisation and travelling to a declared conflict zone.
Of the latest group of arrivals, Home Affairs Minister Tony Burke said on Tuesday seven women and 12 children had made plans to travel from Syria to Australia.
Left behind was another Islamic State-linked Australian woman, who has been issued a temporary exclusion order, according to media reports.
She was barred from boarding a flight after she bought airline tickets for herself and her daughter.
Her child, who is not subject to the order, is understood to have chosen to stay with her.
In a statement on Tuesday, Mr Burke said the government would not provide any assistance to the group.
"These are people who have made the horrific choice to join a dangerous terrorist organisation and to place their children in an unspeakable situation," he said.
"Any members of this cohort who have committed crimes can expect to face the full force of the law."
The government's priority is the safety of the Australian community, Mr Burke said.
