The head of the Australian Sports Anti-doping Agency (ASADA), David Sharpe, said the athletes were caught during pre-event testing along with "a number" of international competitors.
Sharpe declined to name the athletes, saying he could not identify them under laws governing ASADA.
He said a taskforce had been designated to test athletes at home and abroad to make sure the Games were clean.
"That's what it's about, it's about removing the ability of those cheats in sport to have their moment," Sharpe said.
