Thirty-one domestic flights have so far been cancelled out of Melbourne, mostly because of the weather. No international flights have been affected at this stage.

Both Melbourne and Sydney airports have just one runway open for domestic flights, meaning fewer planes can land.

Qantas said it had cancelled about a dozen domestic flights by early Friday afternoon.

Read more: Trees, power lines come down as strong winds batter Illawarra

"We're asking customers to check their flight status for updates and we hope to get everyone to their destination today," a Qantas spokesman said.

Other passengers were hit with delays and long queues at the airports.

One Qantas flight spent more than an hour extra in the air, circling above Sydney Airport before landing at 10.28am. Data on the Flight Aware website says QFA402 travelled 1413 kilometres from Melbourne, almost double the planned 730km.

Airlines were warning passengers to check their flight status on Friday.

"There's windy weather about, which is affecting services across our network. Sorry, we know this blows," Virgin Australia said on Twitter.

Jetstar said strong winds in Sydney had caused cancellations and delays to domestic flights.

"We thank customers travelling to or from Sydney for their patience and advise them to check the current status of their flight," a Jetstar statement said.

"We appreciate delays are frustrating, however safety is our highest priority."

Jetstar passengers will be contacted by SMS.

The Age