Dozens of flights to and from Sydney have been cancelled as wild winds batter the airport for a second day in a row.

Three passengers were taken to hospital and nine others assessed by paramedics after turbulence on board a flight from Honolulu to Sydney on Friday.

Almost 40 domestic flights had been cancelled by Saturday morning.

Air traffic controller Airservices Australia told the airport it was likely just one runway would be operating later in the day due to strong winds.

Thousands of passengers were left scrambling to find new flights on the first day of NSW school holidays.

A spokesman for Sydney airport said any passengers with concerns should speak to airlines directly.

Hawaiian Airlines has been contacted for comment.

-AAP