Sports Minister Sussan Ley and Australian Sports Commission chair John Wylie have written to the top-funded organisations threatening cuts if "gender-neutral" travel is not introduced.
The commission will provide US$94 million in funding to sports organisations in the year to June.
"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," the letter says.
Ley told the Australian Broadcasting Corporation: "Quite frankly I was shocked and surprised to find that in every sport it isn't always the case that the guys and the girls fly and are accommodated at the same level of travel."
"I am prepared to tie the funding to compliance with this but I don't expect it to come to an argument. I know it won't, in fact."
Media slammed Basketball Australia when it was discovered that the Opals female team travelled economy to the 2012 Olympics in London unlike the men who flew business, despite being less successful.
She also called for gender-neutral progress in domestic sports leagues and for elite level mothers to get help.
"If you are competing at that level and your child needs to travel with you, of course arrangements I'm sure would be made. That is common sense," she said.
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