The passport control system went down at about 6am on Monday morning.
A spokesman for the Australian Border Force said it was working with the Home Affairs Department to try and "resolve an IT systems outage impacting inbound and outbound passenger processing at international airports".
In a statement posted on its Facebook page, the ABF said: "Additional ABF staff have been deployed to process passengers and to minimise delays.
One passenger told the 3AW radio station she had been stuck in immigration queues at Melbourne Airport for half and hour and barely moved two metres.
"It seems as if all the e-machines have gone down, so they have to manually process everyone," she said.
@flySYD so, Sydney Airport you should be ashamed. 7am, all the international flights are landing, the epassport gates aren't working and 2000 people are jammed into your poxy arrivals hall. pic.twitter.com/lsGJy5Wmv0— David Berger (@davebergie) April 28, 2019
“About four planes have landed, I reckon there’s 500-600 people here. It’s just ridiculous.”
Melbourne Airport said on Twitter: "Due to an @AusBorderForce e-gate system outage many international travellers are facing delays for both inbound & outbound processing. This may have a flow on effect inside security screening in Terminal 2, while the issue is being resolved.
"Travellers should still arrive as per normal for scheduled services and speak to their airline for updates. We’re extremely appreciative of the patience shown by passengers this morning & we would like to thank everyone for sticking with us during this period."
⚠️ Due to nation wide outage of Border Force smart gates, delays are being experienced to arrivals and departures at the International Terminal. We thank you for your patience at this time. Please check flight status with your airline. ⚠️ https://t.co/OP0JMMLUwR— Brisbane Airport ✈️ (@BrisbaneAirport) April 28, 2019
Update: The issues dogging the SmartGate system were resolved by Monday afternoon.