9News vision shows the drone in extremely close proximity to an F-35 jet worth nearly $80 million.
A photographer who took an image of the incident said the drone was so close to the fifth-generation fighter, it was flung aside by the jet wash.
“People just need to understand that if you have a drone … that you just need to keep them away from the flight paths and the airports, or air shows like this because the consequences of an impact could be catastrophic,” Captain Mark Hofmeyer from the Australian and International pilots Association said.
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The Department of Defence and the Civil Aviation Safety Authority are both investigating the incident.
CASA has reminded drone users to act responsibly and safely.
The flyover took place half an hour before the Supercar races at the weekend.