Sydney, Melbourne and Brisbane airports are experiencing widespread delays and cancellations, with some passengers being told they will not be able to fly until Tuesday.
Sydney Airport said many of their delays and cancellations were pre-emptive as strong winds could close one runway about 11am.
It comes as New South Wales, Victoria and Queensland students are all on school holidays.
Virgin Australia passengers seem to be experiencing the most cancellations.
Passengers told 9News Virgin staff said the cancelled flights were due to air traffic control issues.
Many are worried about missing connecting flights including a cruise departing from Brisbane and other international destinations.
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One passenger told 9News their family would not be able to get on a new flight until Tuesday so they were now going to have to drive home to the Central Coast and lose a lot of money.
A group of eight said they were placed on numerous flights but were now going home about $20,000 out of pocket.
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9News.com.au has contacted Qantas, Virgin Australia and Jetstar for comment.
