"Our Australian basketball teams, the Opals and the Boomers, both play the same game, they're both tall and they are both equally committed to representing Australia at the Games. They shouldn't have to travel a different class because they're both world class."
Australian chef de mission Nick Green said sports governing bodies were given funding to provide each Olympian a return economy airfare with Qantas.
It was up to the those bodies, including Basketball Australia, to decide how they allocate their funding, he said.
A Basketball Australia spokeswoman told the Melbourne Age the travel arrangements were partly down to the height difference between the teams.
"Different factors are taken into account when organising travel arrangements for our national teams - height and size being a primary consideration.
"For example, the average height of our male basketball players is 200.2cm. The average height of our female basketball players is 183cm," she said.
The spokeswoman said it was up to the individual teams to opt how to spend their budgets for the games.
She could not say whether The Boomers had a larger budget than The Opals.
The Boomers have an agreement with Basketball Australia allowing them to travel business class for any flight over three hours, while The Opals do not, the Melbourne Age reported.
Japanese team officials are also under fire for making their country's world champion women's soccer team fly economy while the less celebrated men's team rode business class.
The Japanese women's team was awarded business class seats on their return home from winning the World Cup in Germany last July.
However, the Japanese Football Association reinstated its policy of putting all female athletes in economy class for the Olympics.
Its star player Homare Sawa complained about the policy to Japanese media.
"I guess it should have been the other way around," she said. "Even just in terms of age, we are senior."
