More than 150 flights passing through Sydney airport have been affected, including 95 across the Qantas network, as the airport struggles with staffing shortages.
Virgin flights were also affected.
A spokesperson for the airport said Airservices Australia, which oversees air traffic control there, was managing reduced air traffic movements expected to impact flights network-wide and result in delays.
"We encourage passengers to check with their airline for the latest information on their flight," they said on Saturday.
Airservices Australia said it had enacted air traffic-flow management measures, including spacing out departures, due to roster constraints.
It acknowledged this may cause disruptions but added that it was working with airlines to reduce the impact on passenger travel. Â
"Airservices is enhancing our training pipeline to add further controllers to improve roster depth and is working to address rostering issues that reduce the flexibility of our workforce," a spokesperson said.
Stephen Beckett, the CEO of Airlines for Australia and New Zealand, told the ABC that Airservices Australia had been unable to roster enough staff three days in a row.
"They continue to tell us they have recruited enough people to staff the power. If so, why do we have these persistent problems?" he said.
"The problem in the tower has been going on for years and Australian travellers are having enough of it because these are entirely preventable delays."
Mr Beckett called on Airservices Australia to identify the root cause of the issue and detail plans to address it.
"We need Airservices Australia to support their people and ensure they have enough human resources and other resources to ensure the towers are adequately staffed."
The country's busiest airport also faced significant delays on Friday, with some passengers forced to sit on the tarmac for over an hour as more than 120 flights were delayed.
Airservices Australia has previously said air traffic controllers are dedicated to performing a demanding role.
"We take their wellbeing and psychosocial safety seriously and ask that commentary on operational performance recognises the professionalism and commitment of the controllers working every day to keep the travelling public safe."
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