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The airline is citing alert level uncertainty but travellers say flights still in the system are much more expensive.
One customer said the airline was ''currently doing mass cancellations'' of domestic flights in three weeks time, at a time when many university students are on the move.
The airline said on Wednesday afternoon it had made the call that travel in and out of Auckland was unlikely before December 6 so had cancelled flights to give customers more time to re-plan their travel at a future date when flying was more likely.
'The customer said some replacement flights had been given a new flight number and the price put up by three times.
Another passenger on Tuesday got a message from Air New Zealand saying their December 5 Auckland to Wellington flight and return or connecting flights in the same booking were cancelled.
However, the customer found online there was one flight still available for December 5 but the fare was $185 for a seat only and $205 for a seat and bag.
Their original flight was two hours earlier and priced at $59 for a seat and $69 for a seat and bag.
At alert levels 3 and 4, flights out of Auckland are limited to a skeleton service for essential workers but there has been no announcement on when the restrictions will be lifted.
When outlining the trafffic light system last Friday, Prime Minister Jacinda Ardern said the Government was actively exploring domestic travel out of Auckland once it passed milestones including 90 percent vaccination rates.
A Commerce Commission spokesperson said it had received five complaints about Air NZ's cancellations, which were being assessed.
In general terms, the main factor that will determine a consumer's rights or a business's obligations when travel cannot take place will be the terms and conditions that were agreed to at the time of the booking or transaction.
Some contracts will provide rights to a refund; others may state that a credit will be provided, allowing consumers to rebook at a later date.
Another Auckland man anxious to see his daughter in Wellington after months of lockdown said he wanted to know whether Air NZ knew more about any changes to travel rules than the public.
''I was angry that Air NZ cancelled our flights in November and December without warning. As far as I am aware there is no timeline as to when Aucklanders will be able to fly to Wellington,'' he said.
''What do I not know and the people who live in Auckland do not know? That is very concerning in my opinion.''
Another customer said: ''We bought our son the most expensive ticket to travel so we could change flights at no extra cost. Now the new flights offered are over $ 130 more.''
She said buying this type of top tier ticket seemed to favour Air NZ and not the customer because now we are forced to buy a much more expensive ticket.
''Last night (I) waited on phone for 90 minutes before giving up. This is just not on.''
Air New Zealand chief customer and sales officer Leanne Geraghty told The New Zealand Herald a large number of flights had been cancelled due to the Auckland border remaining in place.
"We know how incredibly frustrating last minute flight cancellations have been for our customers,'' she said.
Last year the airline made over 1000 schedule changes, many in response to alert level changes.
''Yesterday we took the view that open travel into and out of Auckland before December 6 was unlikely so we made the call to cancel those flights to give customers more time to replan their travel at a future date when flying is more likely, she said.
If Auckland's border reopens earlier than anticipated, we will stand up additional flights for customers as quickly as possible.
Air New Zealand continues to operate a reduced schedule to allow for the movement of essential workers and exempt travellers around the country. Due to the limited number of seats available the pricing on some of these flights may be higher than the original fare paid, she said.
''If customers are still eligible to travel, they can rebook their flight within a seven day period from date of travel through the contact centre with no additional fare or fees to pay."
The airline says cancellations were made to consolidate its schedule based on the demand it was seeing.
A spokesperson for Covid-19 Response minister Chris Hipkins pointed to the Prime Minister's remarks.
''In the meantime, we need all of New Zealand to be highly vaccinated. Vaccination offers freedom and protection, more certainty for everyone, and it will reduce the disruption COVID has caused in our lives.''