Passengers flying in and out of Sydney experienced average delays of up to 90 minutes after the airport's air traffic control tower was forced to evacuate.
About 20 staff had to leave the tower soon after 11am on Friday after detecting smoke on the ground floor.
All outbound flights were temporarily grounded, and those about to land had to either be diverted or maintain a holding pattern.
Air traffic controllers were cleared to return to the tower just after 12.30pm and operations returned to normal soon after.
"There will be an ongoing impact on the network, but we are trying to facilitate as best we can," Airservices Australia said in a statement on Friday afternoon.
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Sydney Airport experienced average delays of between one hour and 90 minutes for domestic flights.
There were no international cancellations.
Virgin Australia cancelled eight flights, diverted five flights and there had been flow-on delays of about an hour, however operations are back to normal.
A Qantas spokeswoman said the disruption had thankfully occurred at a quieter part of the day.'
"However, there may be some delays for customers of up to two hours as all airlines work to get back to their normal schedules," the spokeswoman said in a statement.
Fire and Rescue NSW Inspector Bryce Jonas said fire alarms were triggered by smoke on the tower's ground floor.
Crews used thermal-imaging detectors to find the source, which appeared to be a battery back-up that had malfunctioned.
A carbon dioxide extinguisher was used to cool it down, Insp Jonas said.
"It could have been disastrous if it was a large fire to such critical infrastructure," he told AAP.
"They did the right thing by self-evacuating."
A number of passengers who were scheduled to fly out were stuck on the tarmac during the incident.
"Sitting on plane, captain says "smoke in @SydneyAirport control tower, fire trucks on scene," Tim Napier posted on Twitter.
"Hope everyone is ok but may mean a slow trip home."
Among those reportedly stranded were members of the Cronulla NRL team.
"General mayhem (at) Sydney Airport with a one hour delay at 11.30am causing epic delays," Hannah Sturrock posted on Twitter.
Ross Bark posted on Twitter it was "ridiculous that Australia's busiest airport can be completely shutdown by what looks to be a fire alarm".
