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The two Boeing 747s had "come into contact with each other during towing" at the Avalon base south of Melbourne, said Qantas general manager of engineering David Cox.
"Both aircraft did sustain some damage and the extent of this is being assessed," Cox said in a statement.
Television pictures showed one plane appeared to have lost its nose-cone, while the other had suffered damage to its wingtip. No one was aboard either plane at the time.
Qantas said it had stood down a number of workers involved while an investigation into the incident is conducted.
The collision is the latest in a series of dramas that has plagued Australia's national flag-carrier in recent months.
In October, a computer glitch caused a Qantas plane to plunge into a 200-metre mid-air nosedive, injuring more than 70 people, with some suffering broken bones.
In July, a Qantas Boeing 747-400 made an emergency landing in Manila after a mid-air blast caused by an exploding oxygen bottle punched a hole in the fuselage during a flight from Hong Kong to Melbourne.
That aircraft, which was undergoing repairs at the base before returning to service, was one of the two damaged in Tuesday's collision.
"I understand that repairs were undertaken in Manila by Boeing and Qantas — further work was being done in Avalon prior to its return to service," a Qantas spokesperson said.
She would not say how close the aircraft had been to returning to the air.
AFP