The two-hour check in time comes after an alleged terror plot was uncovered.
In a joint statement, Qantas and its budget airline Jetstar said they have increased their security measures across Australia.
"Given the additional screening requirements, we ask passengers to arrive at the terminal two hours before domestic flights and three hours before international flights. Passengers are also asked to limit the amount of carry-on and checked baggage where possible as this will help to ensure security screening is efficient," the statement read.
"Australia has very strong safeguards in place at its airports; these changes are about making them even stronger.
"We appreciate the understanding and patience of passengers as we implement these enhanced security measures."
Passengers flying with Virgin were also notified via text and email over the weekend.
"The Australian Government has introduced additional aviation security measures for both international and domestic terminals at Australia’s major airports," the email read.
"The travelling public can expect to experience an increased level of security scrutiny at the airport but they should not be concerned about these precautionary measures.
"As the measures place an additional burden on the screening system, it may take a little longer than usual to get through the process.
"Passengers should arrive at least 2 hours before domestic flights and 3 hours before international flights to allow time for security screening."