The airline said the croc got out of its cage during a Brisbane to Melbourne flight last week and was found roaming the baggage compartment by a handler, The Daily Telegraph, Sydney, reported Monday.
The reptile was returned to its cage without incident, Qantas said.
The airline said logistics company Australian Air Express is looking into whether the cage had been properly secured prior to the flight.
The size of the crocodile was not reported, The Telegraph said.
Exploding whale video goes viral on Internet
Gal Gadot cast as Wonder Woman for 'Batman vs. Superman'