Australia's basketball association came under fire during the London Olympics after it was revealed that the medal-winning national women's team flew economy class to the 2012 Games while the less successful men's side were in business class seats.
Australia's soccer and cricket authorities also offer different travel standards for top male and female athletes.
Federal sports minister Sussan Ley and Australian Sports Commission (ASC) chairman John Wylie wrote to the 30 top-funded organisations demanding changes, state media ABC reported.
"In 2016, we can think of no defensible reason why male and female athletes should travel in different classes or stay in different standard accommodation when attending major international sporting events," ABC quoted the letter as saying.
"The ASC is now proposing to make gender-neutral travel policies for senior major championships a condition of investment by the ASC in a sport."
Professional Footballers Australia welcomed the move as "long overdue".
"The universal values of sport, which are so celebrated, have not been afforded to Australia's most talented sports women," the PFA's Player Relations Executive Kathryn Gill said in a statement.
"Rather they have consistently been treated as second-class citizens rather than the world class athletes they are."
Cricket Australia acknowledged it had different travel standards for male and female cricketers but said it was "committed" to addressing discrepancies in the class of air travel.
(Reporting by Ian Ransom; Editing by John O'Brien)
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