High winds and heavy rain have led to hundreds of travellers being stranded at airports across the country as dozens of flights coming in and out of Sydney are cancelled in the lead-up to the AFL grand final.

Up to 40 flights due to land or depart out of Sydney were cancelled on Thursday morning, leading to further cancellations in Melbourne, as severe weather warnings were issued by the Bureau of Meteorology for heavy rain and thunderstorms across NSW’s east coast.

Delays were expected to get worse in the afternoon, with two runways to be closed due to the rain and wind. That would leave all domestic and international flights sharing a single runway.

“Sydney Airport is expected to shortly move to operating off a single runway due to poor weather conditions,” an Airservices Australia spokesperson said.

“Safety is our No.1 priority.”

Earlier, passengers in Sydney complained on social media of receiving alerts about cancellations at 4.30am, and there were long queues inside the Sydney terminal.

Tweet from @Qantas

The cancellations came after Airservices Australia advised Sydney Airport and airlines on Wednesday night of potential severe weather conditions, a Sydney Airport spokesman said.

He said passengers flying in and out of Sydney should check with their airline on the status of their flights.

“Passengers who are travelling today are recommended to arrive two hours prior to domestic flight departures, and three hours for international services,” the spokesman said.

It is expected 2.4 million people will fly through Sydney during the holiday peak.

Travellers at Melbourne Airport also faced hurdles, with 11 flights cancelled on Thursday, predominantly arriving from Sydney.

Some 86,000 people are transiting through Melbourne Airport on Thursday, with terminals busy but flowing well, a spokesman for the airport said.

As Victorians enjoy two consecutive public holidays before the weekend, a further 90,000 people are expected to travel through Melbourne Airport on Friday and Sunday, with grand final Saturday expected to be a slower day.

Travellers were urged to arrive one to two hours before domestic flights and two to three hours before international flights, the spokesman said.

“Given there are so many people travelling this long weekend, we’re encouraging everyone to allow themselves plenty of time to find a car park, check in and clear security,” he said.

Meanwhile in the Sunshine State, operations were “flowing relatively smoothly” at the Gold Coast Airport, according to a spokeswoman.

She said operations were being assisted by an ambassador program that helped people board flights and check-in at the terminal.

Thursday’s public holiday coincided with the start of school holidays in many states.

Victoria and Queensland are mid-break, while term ends in NSW, the Northern Territory, ACT and Western Australia on Friday.

Tasmania’s holidays start at the end of next week.

-with AAP