The airport chaos affecting thousands of travellers struck as a flight from Honolulu hit "severe turbulence" that injured some passengers.
At Sydney Airport dozens of flights were cancelled by Saturday afternoon due to winds of 45km/h and staffing issues.
More than 100 flights were cancelled on Friday and the disruption has spread to airports across the country.
At Sydney Airport the traffic controller, Airservices Australia, said it was likely just one runway would be operating later on Saturday due to strong winds.
A spokesman for the airport said any passengers with concerns should speak to airlines directly, as thousands scrambled to find new flights on the first day of NSW's school holidays.
"Airlines are working hard to re-accommodate passengers and get them on their way," an airport statement said
On Friday evening a Hawaiian Airlines flight encountered turbulence that injured some passengers while flying over the Pacific Ocean, the airline said.
The HA451 flight hit strong winds and "unexpected severe turbulence" about five hours into the flight.
"Four passengers and three flight attendants were initially treated by a doctor onboard and our crew members, in consultation with physicians on the ground," Hawaiian Airlines said in a statement.
The Airbus A330 aircraft carrying 163 passengers and 12 crew landed "without incident" at Sydney Airport at 7.47pm on Friday, the airline added.
"We conducted a thorough inspection of the aircraft before boarding HA452, which departed Sydney to Honolulu at approximately 10.30pm local time yesterday."
NSW Ambulance paramedics assessed 12 patients at the scene while three were hospitalised with injuries including back pain.
Two passengers were taken to St George Hospital while another was transferred to Royal Prince Alfred Hospital, a NSW Ambulance spokesperson told AAP.
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