Heavy rain from ex-tropical cyclone Debbie is causing havoc for flights in and out of several major airports in Queensland and parts of NSW.
Virgin said its flights to and from Ballina, Coffs Harbour, Newcastle, Port Macquarie in NSW may also be affected by wet weather today.
Passengers booked on Virgin flights to or from Brisbane, Bundaberg, Gladstone, Sunshine Coast and Rockhampton in Queensland could also be delayed by the wet weather.
Comment was being sought from Jetstar.
Earlier, Virgin Australia has cancelled domestic flights at Queensland's Gold Coast and Prosperine airports, while no Qantas flights will operate to or from Gladstone.
However, Qantas has resumed some Hamilton Island flights to help evacuate hundreds of tourists stranded as a result of cyclone Debbie.
A spokesman said the remainder of its flights across Queensland were operating as usual.
Virgin Australia said there would be no flights in or out of Prosperine, near the cyclone-ravaged Airlie Beach, on Thursday or Friday. All its domestic Gold Coast flights scheduled to arrive or depart this afternoon were also cancelled.
The airline is meanwhile working with authorities to confirm whether it is safe to fly in and out of Hamilton Island.
"Due to the extensive damage to infrastructure on the island, Virgin Australia will not bring any more guests into Hamilton Island for the next two days, up until and including Saturday 1 April," the airline said in a statement.
"An update on inbound services to Hamilton Island from Sunday 2 April onwards will be provided following further assessment."