The remnants of the team left a Gold Coast hotel on Tuesday afternoon under police guard with one player appearing to be dragged by a teammate onto the bus bound for the airport in a video published by Nine newspapers.
Protesters attempted to block the bus amid safety concerns for the women returning to Iran after arriving at a Gold Coast airport a short time later.
Australia had knocked back the visas of some officials, sources familiar with the matter told AAP, but there were concerns that handlers were coercing the remaining players to return to Iran and not apply for asylum.
The Home Affairs Department would not confirm how many visas were refused on security or character grounds, citing privacy restrictions.
"The Department of Home Affairs works with law enforcement and intelligence partners to cancel or refuse visas of non-citizens who are at risk to Australia's national security," a spokesperson said in a statement.
A sensitive operation has taken place to circumvent the players' restrictive handlers and separate those looking to escape.
The women, who have been in Australia for the Asian Cup tournament, faced retribution after they were branded traitors on Iranian state media for refusing to sing the national anthem before their first match.
The five players were being kept safe by Australian Federal Police, Prime Minister Anthony Albanese said earlier.
"Australians stand in solidarity with these brave women, they are safe in Australia and they should feel at home here," he told parliament on Tuesday.
"We have made it clear that if there are other members of the team who make a decision to ask for support, they will receive it from Australia."
Opposition Leader Angus Taylor declared his support for the visas being granted.
Matildas midfielder Clare Wheeler said her thoughts were with the Iranian team and it was important to shed light on the issue.
"At the end of the day, it's paramount their health and wellbeing is protected," she told reporters in Perth.
Home Affairs Minister Tony Burke confirmed the women had escaped their Iranian handlers while staying at a hotel on the Gold Coast and were moved to a safe house on Monday night.
The visas were granted after security checks were satisfied, and there was an outbreak of "Aussie, Aussie, Aussie, oi, oi, oi" once the applications had been approved, Mr Burke said.
The Lionesses' team captain, Zahra Ghanbari, and players Fatemeh Pasandideh, Zahra Sarbali Alishah, Atefeh Ramezanizadeh and Mona Hamoudi took up the offer of safe haven and gave their permission for their names and pictures to be published.
NSW anti-slavery commissioner James Cockayne urged the AFP to open a human trafficking investigation following reports of the possible coercion of players, including restrictions on their movement while in Australia.
The team's plight prompted the intervention of US President Donald Trump, who used his Truth Social platform to suggest Australia would be "making a terrible humanitarian mistake" by allowing the women to be forced back to Iran.
He later congratulated Mr Albanese for protecting the women after a late-night call between the pair.
"He's on it! Five have already been taken care of, and the rest are on their way," Mr Trump wrote.
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