Gusts of up to 70km/hr are expected to sweep Sydney Airport today, peaking between 9am-3pm today.
So far, more than a dozen flights from Qantas, Jetstar and Virgin have been cancelled.
The disruptions yesterday were blamed on a number of air traffic controllers taking sick leave, particularly in Brisbane.
Qantas said at least 100 flights yesterday were delayed, leaving thousands of passengers impacted.
A total of 10 of the airline’s flights were cancelled outright.
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Virgin said its affected flights were mostly across Brisbane, the Gold Coast and Ballina.
Most of the delays took place from about 6am with knock-on effects through to 1pm, covering the busy morning and lunchtime rush.
Adding to the potential for chaos today and across the weekend is the beginning of the NSW school holidays, with today being the last day of term.
Already a number of flights across Virgin and Jetstar have been cancelled this morning.