Passengers were unable to be processed at the T-1 global or T-2 domestic terminals - leaving hundreds stranded.
'Arrivals into Sydney are running as usual, and departures are expected to be operating as normal from midday onwards, ' he said.
If there's anywhere you would want to avoid this morning, it would be Sydney airport... Almost 16 million of those were global passengers, with those from China being one of the major sources of travellers, according to airport figures.
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Passengers are being urged to avoid these terminals as the airport staff work to resolve the issue.
Virgin Australia said it was holding some flights to minimise disruptions and was working to re-accommodate those affected.
The issue prevented passengers from being processed for about two hours, but Sydney Airport said it had resumed screening just after 7.30am.
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The Airport's Sally Fielke says the issue has been fixed by airport technicians and the software provider.
At around 7:45AM Sydney Airport Tweeted that it was once again processing passengers in the affected terminals.
Virgin Australia flights were also recovering from significant delays, which included two cancellations.
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A spokeswoman for Qantas told Daily Mail Australia terminal 3 had not been affected, and flights were running as normal.