"The long tail of Covid" and engineering issues are continuing to disrupt flights across the country, while airlines and airports face high demand as the school holidays begin.
Air New Zealand has brought back its flexibility policy to ease some of the pressure, with more than 2500 people swapping their tickets for credit already.
Six of the airline's flights into Auckland and four flights out have been cancelled this morning.
Last week the airline warned of three-hour waits to get through to its call centre.
While there have been long queues in Auckland, operations have been running more smoothly at Wellington and Christchurch airports.
Christchurch Airport's chief aeronautical and commercial officer Justin Watson said there had been a few cancellations, caused by weather, engineering issues and "the long tail of Covid-19" which was affecting crews and pilots.
So far two flights from 80 flying in or out of Christchurch Airport today had been cancelled which was not huge "but still disruptive".
Watson said once flights were cancelled, passengers might have to wait a day or so to get another seat because most flights were full.
"It's an unfortunate situation brought about by Covid and there's not a lot we can do about it when people are getting sick and having to isolate."
'It's great to see everyone travelling again' Wellington Airport's head of operations Matt Palliser
Wellington Airport's head of operations Matt Palliser said it had been a busy start to the school holidays with an average of 25,000 travellers per day, the highest numbers since the Covid-19 pandemic began.
"It's great to see everyone travelling again."
Palliser said travellers were being advised to check flight schedules online, check-in online if possible and arrive at the airport early for bag dropoff and to get through security.
Both men said the Ministry of Health has mandated mask use and there was high compliance within the airports and on flights.
"A lot better than you see out in the general public," Watson said.