Air New Zealand is blaming its computer system crash on supplier IBM, which it says fell "well short of expectations".
An IT outage crashed airport check-in systems, as well as online bookings and call-centre systems about 9am yesterday, affecting more than 10,000 passengers and throwing airports into chaos.
Flights at Dunedin International Airport were still running about an hour late by mid-afternoon.
Six flights were affected at Queenstown airport and one at Wanaka.
Most systems were restored early yesterday afternoon, but the passenger backlog did not clear until self check-in kiosks were running again about 3.30pm.
"We are sorry customers faced delays of up to two hours as we used manual processes for check-in and boarding," Air New Zealand short-haul airline group general manager Bruce Parton said.
The company appreciated the patience customers had shown, particularly as many were travelling with children at the end of school holidays, he said.
The IT outage at the IBM-run central computer facility affected other businesses as well, he said.
"We are deeply disappointed by the performance of this supplier, who has fallen well short of the expectations we have on behalf of our customers," Mr Parton said.
It would be investigated further today, he said.