The trio is part of a larger group including children who boarded a flight in Damascus before landing in Sydney and Melbourne on Thursday evening.
Years ago, the women travelled to the Middle East with their partners who intended to fight for Islamic State.
There were chaotic scenes upon their arrival: in Melbourne, 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 total, three women will be charged with eight offences, AFP Assistant Commissioner Stephen Nutt told reporters in Canberra on Thursday night.
They include a 53-year-old, arrested in Melbourne who is facing four crimes against humanity - slavery charges, including keeping and using a slave, and engaging in slave trade.
A 31-year-old woman, also arrested in Melbourne, is facing two slavery charges.
In Sydney, a 32-year-old woman was charged late on Thursday night with entering a declared area and joining the Islamic State group.
The 32-year-old was expected to face Downing Centre Local Court on Friday.
Once the two others are formally charged, a court date will be locked in.
Further investigations into the group are ongoing.
The senior AFP officer would not answer questions 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 the group of young people is 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.
Education Minister Jason Clare said the government had confidence in federal police's ability to protect the community from any potential risks.
"This is not their first rodeo. The Federal Police have done this before," he told reporters in Sydney on Thursday.
It would take time for the children to be able to go to school and take other steps to integrate into Australian society, and that would be guided by police, Mr Clare said.
The senior minister added that while nobody would have sympathy for anyone who supported Islamic State, the young people involved had no choice in who their parents were, and the trauma they have experienced would be with them for some time.
