Ian Chesterman, Australia's chef de mission, told reporters Wednesday that he had received a report from Japan Airlines about the "unacceptable" behavior of team members.
Athletes "failed to respond to requests for them do do whatever they needed to do on the flight," Chesterman said.
"And then there was also the issue of at least one person being sick in the toilet and leaving that inoperable for the remainder of the fight," he added.
CNN has reached out to Japan Airlines for comment.
Both Football Australia and Rugby Australia have launched formal investigations into the conduct of personnel on the flight, Chesterman said. Disciplinary action might follow when this process is concluded, he added.
"Can I also say how deeply disappointed I am in this behavior. This behavior clearly is unacceptable and does not meet the standards set by this team," Chesterman said, adding: "This is a proud team, performing brilliantly after a very very challenging preparation and the vast, vast majority have conducted themselves superbly both on and off the field of play."
He said some people had made poor choices but that he hopes they will make better choices in the future.
As of Wednesday, the Australian team was fourth in the Tokyo 2020 medals table, winning a total of 36 medals: 15 gold, four silver and 17 bronze.