Outbound passengers at Sydney's T1 worldwide and T2 Domestic terminals were prevented from checking in for their scheduled flights, and airline staff were reportedly processing some passengers manually.
Meanwhile in Brisbane a passenger set off a security screen at the worldwide terminal, causing a backlog of commuters.
Jetstar expects all their flights will be back on schedule by midday, after its morning flights were delayed by an hour on average.
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A technical problem hit the air hub of Australia's New South Wales state capital on Friday, when flight delays left crowds of global and domestic passengers stranded for hours, according to Sydney airport authorities.
Around 6.30am, Sydney Airport reported technical difficulties at the two terminals and urged passengers to be patient.
The other domestic terminal, T3, is operated by Qantas and is not experiencing an issue.
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Sydney Airport is advising passengers to check with their airline for up-to-date information about their flights.
The airport is yet to estimate when the issue will be completely resolved.
"We hope to have the area cleared shortly to recommence screening", Brisbane Airport tweeted.
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A spokeswoman for Brisbane Airport told the Courier Mail security screens were closed for 30 minutes after the breach.
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