The Boeing 737-838 first took off about 6.45am before turning around over the Tasman Sea and returning to Christchurch Airport.
A Qantas spokesperson says pilots chose to return due to an issue with their radio, which was fixed by engineers before taking off again for Melbourne.
But following a second departure around 9.40am, the plane again turned back to Christchurch, this time due to an unusual smell in the cabin.
The spokesperson says the two incidents are unrelated.