Athletes returning via Sydney to the state of South Australia are facing an extra two-week quarantine.
That is on top of the two weeks already required for all overseas arrivals.
The AOC said: "While other countries are celebrating the return of their athletes, we are subjecting ours to the most cruel and uncaring treatment."
They added: "They are being punished for proudly representing their country with distinction at the Olympic Games."
16 members of the Australian Olympic team are already quarantining in Sydney, the capital of New South Wales.
