Home Affairs Minister Tony Burke on Wednesday confirmed humanitarian visas were granted to a player and a support worker, bringing the total number of members staying in Australia to seven following the team's exit from the Asian Cup.
He confirmed Australia offered asylum to all the athletes, and that government officials did not rush or pressure them into making a decision.
"The one pressure we couldn't take away was the context … what pressures they might have felt with their own family members," Mr Burke told reporters in Canberra on Wednesday.
"We should be proud that we're that sort of country for the seven people who've decided to take up that offer.
"They are now on humanitarian visas, and the processing will soon start for them to move to what's called a resolution of status, which is a permanent visa."
The Iranian players also asked Mr Burke to help their families get out of Iran.
"The challenge with Iran is we can't even get Australian citizens, necessarily out of Iran," he said.
"And I was very up-front in my meetings with people, because they'd ask me, 'Can I now help their family members if I help them?'."
There are fears for the rest of the team's safety on their return to Iran after they were labelled "wartime traitors" on Iranian state media for refusing to sing the national anthem before their opening match.
Mr Burke said he couldn't provide details on what the fate of the returning women could be.
"We didn't talk in this precise terms, but I'm very mindful of the different comments that have been made by the Iranian Australian community," he said.
Mr Burke said the two people granted asylum were reunited with the first five in Sydney overnight.
The team had left a Gold Coast hotel on Tuesday afternoon under police guard with one player appearing to be dragged by a teammate onto the bus, according to a video published by Nine newspapers.
Mr Burke said the footage made it clear that each person had to make their decision without anyone else from the delegation near them.
Protesters tried to block the bus from leaving for the airport.
Not everybody who was part of the Iranian soccer team delegation was granted a visa to enter Australia for the Asian Cup, Mr Burke said.
"People who are connected to the IRGC (Islamic Revolutionary Guard Corps) were not granted visas in terms of that sort of connection," he said.
"There were also some people leaving Australia who I am glad they are no longer in Australia."
The team members previously confirmed to be staying in Australia were captain Zahra Ghanbari and players Fatemeh Pasandideh, Zahra Sarbali, Atefeh Ramezanizadeh and Mona Hamoudi.
Iranian refugee advocate Ara Rasuli, who was involved with the asylum process, said the Australian government had "opened every avenue for the girls to stay here and to be protected".
The players who returned to Iran possibly faced execution and their families faced retaliation from the regime, she said.
"They are in a lot of danger," Ms Rasuli said.
"There are all sorts of different threats, such as taking the families into custody, taking over their assets ... and that's why most of the girls are choosing to go back home, because the threats are a big issue in this matter."
