Passengers are being asked to arrive at least two hours early for domestic flights, with Sydney Airport saying about 82,000 passengers will need to get through security gates and check-in counters.
Sydney Airport has been under pressure for a week from staff shortages and absences because of COVID-19 infections, resulting in long check-in queues.
"I know it's a difficult message to hear but Thursday is going to be another tough day for travellers, and I want to apologise in advance to anyone who is inconvenienced," Sydney Airport CEO Geoff Culbert said.
Other airports are expected to be under increasing strain over the school holiday period with consecutive long weekends for Easter and Anzac Day.
Tourism and Transport Forum CEO Margy Osmond said after two years of constant disruptions to peak holiday periods from lockdowns and border restrictions, the surge in holiday bookings this Easter was welcome.
"The pent-up demand created by the Omicron outbreak ruining the Christmas and summer holiday plans of many ... is also helping to drive the travel rush," she said.
Nearly one million travellers are expected to pass through Sydney Airport, which is Australia's biggest domestic and international travel hub.
Transport Workers Union National Secretary Michael Caine said baggage handlers, ground staff and security workers were under incredible pressure.
Many of those workers lost their jobs at the start of pandemic lockdowns as they did not qualify for federal government JobKeeper payments because they were employed by foreign companies.
"That's the underlying reason that we're seeing the staff shortages that are leading to this kind of day, with catastrophic scenes at our airport (in Sydney)," he told the ABC on Thursday.
While he acknowledged absenteeism due to the virus was a factor, Mr Caine blamed the Morrison government for denying JobKeeper payments to most airport workers.
He also blamed airlines for outsourcing the jobs of ground staff, like baggage handlers and security workers, to foreign companies in the first place.
"Those 2000 workers are ready, willing and able to come back to work but Qantas is not putting them back on, and now we're seeing this panicked response," Mr Caine said.
It was hard to attract workers back into the aviation industry because of "a degradation of terms and conditions ... so there really is a problem", he added.
The union is calling for an independent commission to address the long term issues in the industry.
Melbourne Airport CEO Lyell Strambi urged travellers to be patient as the aviation industry adjusts to flights picking up again following a nationwide relaxation of coronavirus social restrictions and border closures.
"COVID-19 decimated airlines and airports and resulted in thousands of highly skilled workers being stood down or made redundant," he said.
"Airlines and their suppliers are now scaling up their workforce but given the safety-critical nature of the jobs they do, recruitment and re-training can take time".
Melbourne Airport is forecast to see around 380,000 people go through over the next five days.
Adelaide Airport expects 25,000 travellers to enter its recently expanded terminal on Thursday and a similar number on Friday.
Brisbane Airport expects around 50,000 passengers.