Passengers took to social media to lash out at the airlines, claiming they had been left in the dark.
"I feel like screaming," one Twitter user wrote.
"Daughter in Sydney did all the right things. Double vacc, boostered, PCR test, Qld border pass. Jetstar just cancelled her flight to Bris. No explanation."
In a statement, Jetstar said a "large number" of their frontline workers were having to test and isolate as COVID-19 close contacts in Sydney and Melbourne, forcing some "late adjustments".
"We appreciate the frustration this causes, especially as customers are travelling for Christmas, and sincerely apologise for the impact these changes are having on travel plans," the statement read.
"We are working to minimise any delays and re-accommodating passengers on flights as close as possible to their original departure times across both Jetstar and Qantas services."
Virgin Australia is also reported to have made some changes to its schedule.
9News.com.au has contacted Virgin Australia for comment.
Qantas has cancelled a small number of flights, but it is understood this was due to lack of demand.