Global and domestic flights were both affected by the fault in terminals one and two, with passengers and staff alike not able to pass security.
Their longest delay was two hours, and delays are now running from between 30 to 90 minutes.
'There will be some impact to our flights today as a result.
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.
Photos posted to social media show thousands of people stuck in standstill queues.
POLICE have flocked to Brisbane International Airport to deal with an ongoing "security matter" that has caused security screenings to be cancelled.
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"We're advising passengers and visitors to avoid T1 and T2 until further notice".
Sydney Airport said the technical issue was affecting passenger processing at the T1 global and T2 Domestic terminals up until about 8:30am.
Inbound flights and Qantas flights from T3 remain unaffected.
At about 8:30am, Sydney Airport reported they had resumed processing passengers as normal and were "working hard to catch up on delays", a Tweet from the company said.
Australian Federal Police officers are investigating the matter.
All planes yet to take off were instructed to disembark so passengers could be re-screened.