Passengers caught up in a three-hour system outage at international airports in Australia and New Zealand say the check-in queues were the longest they have seen.

There were scenes of chaos at Sydney and Melbourne airports on Monday, as airline staff had to manually process customers after the globally-used, border-clearance system suffered a major outage.

The system, known as Advance Passenger Processing went down about 8am on Monday and was not fixed until about 11am.

Photos uploaded to social media show queues snaking the length of airport foyers in Sydney and Melbourne, as staff worked to clear the backlog.

A Sydney Airport spokeswoman said its system came was restored at 10.40am, while Melbourne’s was again online by about 11am with all airlines able to process digital check-ins.

“Thanks for your patience this morning. Most airlines are now checking-in for flights. Delays may take a while to work through the system,” Melbourne Airport tweeted at 10am on Monday.

Brisbane Airport was also affected by the shutdown, prompting manual check-ins but no flights were delayed, a spokeswoman told AAP.

Six flights departing from Auckland Airport experienced minor delays when Immigration New Zealand’s national system also went down, according to the Auckland Airport Twitter account.

“Immigration NZ advises the system is now fully functional. Customs arrivals Smartgate will be limited for flights ex Australia that departed during the outage,” the airport tweeted.

People flying internationally were advised to contact their airline to check the status of their service.

All international flights to and from Australia are subject to mandatory APP reporting provided by airlines through the APP system, according to the Department of Immigration and Border Protection.

“This facilitates a more streamlined border clearance process for travellers and enhances the Australian Government’s ability to target security concerns,” the department’s website states.

Passenger Chris Walker-Bush tweeted his frustration earlier on Monday.

“Nobody able to check-in at Sydney Airport. Nobody. I’ve never seen lines this long in an airport,” he said.

Traveller Andrew Jessup tweeted a photo of the “huge queues” captioned: “Bedlam at Sydney Airport”.

Bedlam at Sydney Airport as passport checking stem down. Huge queues, several news crews. pic.twitter.com/B1RsLy9YbS

— AJ (Parroty) (@whenfalse) May 22, 2017

All international flights to and from Australia are subject to mandatory APP reporting provided by airlines through the APP system, according to the Department of Immigration and Border Protection.