The Australian Aboriginal flag and the Torres Strait Islander flag will be on display at all 35 matches across Australia, with the Māori flag, known as 'Tino Rangatiratanga', to feature at all 29 matches in New Zealand.
"Confirmation by FIFA that all official flags of Australia will be flown during the FIFA Women's World Cup is an important moment for all Australians, particularly First Nations People," Football Australia boss James Johnson said in a statement.
Australia's World Cup squad includes Indigenous Australian players Kyah Simon and goalkeeper Lydia Williams.
"For me, obviously, I'm proud of our culture and our First Nations people in the country," Simon told reporters in Melbourne this week.
"Every major tournament, my family's come along and brought their own Aboriginal flag and for me that's obviously a part of my history and my culture and to see my family in the crowd, obviously holding up the flag as well, is something that's close to home for me.
"I'm hoping that people that come from abroad can see that rich culture that we do have here and also be educated along the way."
The World Cup starts on July 20.
