Immigration New Zealand's (INZ) national system went down on Monday, delaying check-in at Auckland International Airport.
It was part of a global outage which also affected Australian airports, an Auckland Airport spokesperson told Newshub.
INZ says the Advance Passenger Processing (APP) system stopped working at about 9:30am on Monday. It was restored just after 1pm.
"The system was out of action for three hours this morning as a result of a global issue," INZ confirmed in a statement.
While it was down, INZ used "manual back-up systems, which could cause some delays to passengers checking in for flights to New Zealand from overseas and when they arrive in New Zealand", national border manager Senta Jehle said.
"When passengers check in overseas, APP validates their entitlement to travel to or through New Zealand. Passenger information entered into airlines' systems is screened against INZ's database at time of check-in."
As a work-around, check-in agents had to rely on manually checking with INZ staff to verify the passengers' information.
The airport confirmed the situation in a tweet, thanking those affected for their patience.
Auckland Airport's website showed more than a dozen flights, mostly from Australia, had been delayed. Others were rescheduled.
Wellington Airport was also affected. It warned some international passengers may experience delays and to check with their airline for the latest information.
Christchurch Airport was also doing manual check-ins, but didn't anticipate there would be significant delays.
Meanwhile, Sydney and Melbourne airports have also experienced delays.