Some athletes also showed "unacceptable behaviour" on their flight home, officials added.
But Australia team boss Ian Chesterman said no disciplinary action would be taken as the athletes had apologised.
He added that the damage was "minor" and that it was "not the hardest thing to break the cardboard bed".
Chesterman did not name the athletes or the sport they represented.
But the Australian Olympic Committee said the national governing bodies of football and rugby union were investigating reports of rowdy behaviour on a flight into Sydney last Friday.
Chesterman said: "Some young people made a mistake - they had left the rooms in a condition that was unacceptable."
He added: "The rooms were not completely trashed in any way.
"It is a book as old as time: a good young person makes a mistake, chapter two is a good, young person is full of remorse.
Rugby Australia said it had launched its own investigation after being informed by Australian team officials of "unacceptable" behaviour by rugby and football players on the flight home from the Olympics.
"Rugby Australia has been made aware of incidents involving the Australian men's sevens programme after being informed by the Australian Olympic Committee," it said.
Matt Carroll, chief executive of the Australian Olympic Committee, said there had been no formal complaint from the airline operating the flight, but added that "unacceptable behaviour was brought to our attention".
He said: "It's extremely disappointing, but both rugby and football [governing bodies] have told me that such behaviour is certainly not acceptable within their sports and have sincerely apologised to the Australian Olympic team.
"The CEOs have undertaken to take the appropriate action and report back to us."
Australia's men's rugby sevens team reached the quarter-finals at Tokyo 2020, losing to eventual winners Fiji.
The men's footballers were eliminated from their tournament in the group stage. The women's footballers are not implicated as they are still at the Games - they face the United States in their bronze-medal match on Thursday.