Authorities are expecting a backlog of delayed flights at Sydney Airport to clear after a computer glitch forced the cancellation of dozens of flights on Monday morning.
Passengers were left facing hours of delays when the air traffic control software failed about 5am.
A cyber attack has been ruled out as the cause of the shutdown.
As a result Air Services Australia (ASA) reduced traffic capacity to ensure safety standards were maintained.
Some of the country's major airlines have put on extra services to ease the disruption.
ASA said there had been a "system software failure" at Sydney's air traffic control.
One pilot described the Harbour City's skies as being "like a ghost town" to air traffic control as he came in to land.
The ABC understands the fault related to the flight planning system.
"The software fault failed to convert from night-shift operations to day-shift operations, consequently one air traffic control console was operational for the morning peak when in normal circumstances six to eight consoles are operating," an ASA spokesperson said.
"The safety of the travelling public is our first priority and traffic capacity was reduced to maintain safety standards."
This feeds into the radar picture and without it, controllers cannot see which plane is which.
Jan Ibbottson is on holidays from the UK and said it was frustrating her flight to the Gold Coast was cancelled.
"I'm very calm about it, but it's chaos," she said.
Ms Ibbottson said the airlines had not handled the situation well.
About 15 planes can land and depart per hour using manual air traffic control methods, but there are usually about 50 movements per hour.
