A computer problem has forced airport staff to manually process passengers at the T1 worldwide and T2 Domestic terminals.
The glitch affected outbound flights from its worldwide terminal and one of its two domestic terminals.
A spokesman from Jetstar told Daily Mail Australia they are still facing delays of an hour on average, almost five hours after the issue was resolved. We're advising passengers and visitors to avoid T1 and T2 until further notice, ' the statement read.
Sydney Airport said the technical issue was affecting passenger processing at the T1 worldwide and T2 Domestic terminals up until about 8:30am.
Virgin Australia said it was holding some flights to minimise disruptions and was working to re-accommodate those affected.
Officials are urging any passengers who planned to fly from Sydney airport today to call their airline and/or check their flight time and status online.
A spokeswoman for the airport said security screens were closed for 30 minutes as a result of the breach on Friday, leading to a backlog.
Many passengers have taken to social media to share their frustration.
She said Australian Federal Police officers were investigating the matter.
It affected systems including the airport's CCTV, meaning passengers could not be screened for about two hours.