The three women are expected to face court in Melbourne and Sydney on Friday, after arriving on Thursday evening as part of a larger group that included children who boarded a flight in Damascus.
It follows a near decade-long investigation, after the women travelled to the Middle East with their partners, who intended to fight for Islamic State.
Police on Friday charged a 31-year-old and 53-year-old with several offences including crimes against humanity allegedly committed in Syria.
Detectives will allege the older woman travelled to the region with her husband and children in 2014, and was complicit in the purchase of a female slave for $US10,000, and knowingly kept the woman in her home.
It is alleged the 31-year-old also had knowingly kept a female slave in her Syrian home in 2014.
They are expected to faced Melbourne Magistrates Court on Friday.
Police said the pair were detained by Kurdish forces in 2019 and held with other family members in Al Roj Internally Displaced Persons camp.
AFP Assistant Commissioner Counter Terrorism Stephen Nutt said operational planning for the potential return of individuals from the Middle East started in 2015.
"This remains an active investigation into very serious allegations," he said.
There were chaotic scenes upon their arrival in Melbourne as intermittent scuffles broke out between members of the media and a group of men, some wearing masks, who escorted some of the group to a waiting minibus.
Some of the men told media to stop recording, including one who yelled "turn your f***ing cameras off".
Heavily armed police officers kept the groups apart and barked orders at the crowd as the women and children were guided into the vehicle.
In Sydney, a 32-year-old woman was charged late on Thursday night with entering a declared area and joining the Islamic State group and was expected to face Downing Centre Local Court on Friday.
A senior AFP officer would not answer questions on Thursday about the fate of the children, many of whom were born in Middle Eastern prison camps notorious for squalid conditions and the presence of extremist groups.
But they are expected to need significant support to help them adjust to life in Australia and to determine whether they've been radicalised while overseas.
Some of the women travelled willingly to support their partners who wanted to fight for Islamic State, but advocates for the group say others were coerced or only went to the Middle East to keep their family together.
There were still unanswered questions about the financial cost of the cohort returning to Australia, opposition home affairs spokesman Jonno Duniam said on Thursday, claiming it may cost as much as $2 million a year to monitor each person.
"That's a lot of money being spent on managing 13 people who I say we should have done more to prevent coming back in the first place," he told Adelaide radio station FiveAA.
Finance Minister Katy Gallagher said the opposition would have done exactly the same when in government.Â
"We will spend what we need to spend to keep Australians safe," she told ABC Radio on Friday.
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