Would-be commuters were left stuck at check-in early on Friday morning after a technical issue resulted in the security screening being unable to open.
"Our teams are working to get everyone to their destinations as soon as possible", a spokesman told AAP.
As reported by ABC News, technical issues affected passenger processing at the airport's T1 global terminal and T2 Domestic terminal until about 8:30AM when Sydney Airport said that systems were back up and running, and that is was processing passengers again.
A spokeswoman for Qantas told Daily Mail Australia terminal 3 had not been affected, and flights were running as normal.
Jetstar expected the issue to create a backlog of up to two hours throughout the day.
Virgin Australia said it was holding some flights to minimise disruptions and was working to re-accommodate those affected.
The technical glitch and subsequent delays come several months after flights were grounded at Sydney Airport's domestic terminal in September past year, due to a technical fault with an air traffic control system, managed by Airservices Australia.
One passenger reported that passengers on all flights that had boarded but not taken off were offloaded and asked to go through the security screening process again, causing "chaos".
It comes as Sydney Airport was thrown into turmoil this morning when a technical issue caused major delays to flights from terminals 1 and 2, with the airport even going as far as telling passengers to avoid the airport altogether.
The technical failure was resolved about 6.30am, 90 minutes after passengers were initially stranded.
Australian Federal Police officers are investigating the matter.