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.
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Virgin Australia passengers seem to be experiencing the most cancellations.
"Multiple Air Traffic Control shortages occurring across the network over the last two days as well as a reduction to one runway in Sydney yesterday has caused number of crew displacements and operational issues that are now impacting flights in Sydney, Melbourne and Brisbane today," Virgin Australia spokesperson told 9News.com.au.
"More disruptions are expected due to the ongoing impact of the industry wide disruptions over the last two days, and we will continue working to keep our guests updated.
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"All guests impacted by cancellations today are being recovered onto the next available flights.
"We apologise to any guests impacted by delayed or cancelled services, and we are working tirelessly to ensure all guests reach their final destination."
9News understands Qantas is expecting a number of delays due to ongoing impacts of yesterday's operations and restrictions on crew hours.
Many are worried about missing connecting flights including a cruise departing from Brisbane and other international destinations.
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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