Air New Zealand is going to "put a temporary hold on new bookings" to align with the Government's managed isolation facilities which are currently housing thousands of people.
Housing Minister Megan Woods, in charge of managed isolation facilities, said she met with Air New Zealand chief executive Greg Foran to discuss ways to jointly manage the big growth in Kiwis coming home.
"Air New Zealand has agreed to put a temporary hold on new bookings in the short term, as well as looking at aligning daily arrivals with the capacity available at managed isolation facilities," Dr Woods said on Tuesday.
"People who have already booked flights with Air New Zealand will still be able to enter New Zealand subject to availability of quarantine space."
The Government is currently holding nearly 6000 people in 28 managed isolation facilities across the country, and more space is being made available, Dr Woods said.
"Our number one priority is stopping the virus at the border, so everyone must go into quarantine or managed isolation. The Government is also talking to other airlines about managing flows.
"The last thing we need are hastily set up facilities to meet demand, so we must have a manageable number of fit-for-purpose, safe facilities that do the job of stopping COVID at the border."
Air New Zealand chief commercial and customer officer Cam Wallace said the airline is working closely with the Government to help contain COVID-19 at the border.
"We accept this is a necessary short-term measure given the limited capacity in quarantine facilities and we're keen to do what we can to help New Zealand's continued success in its fight against COVID-19."
Wallace said the airline is contacting customers affected by the changes.
The Air New Zealand contact centre is currently experiencing very high demand, he said, and customers are encouraged to contact the airline via its social media channels.
The border is currently only open to returning New Zealanders and residents and each returnee is required to undergo 14 days in managed isolation and must test negative for COVID-19 before being allowed to leave.
Air Commodore Darryn Webb said it's a mammoth task.
"It needs appropriate levels of health and other services nearby, New Zealand Defence Force personnel and extra security to ensure that people are looked after properly and the risk of COVID getting out into the community is minimised."
Webb said the temporary hold on Air New Zealand bookings will ease the current demand on facilities while additional supply is brought on line.
"In the past three weeks we have brought on 10 new facilities for 2000 more people, and have a plan to bring on another 750 places in the coming weeks."
The New Zealand Defence Force is closely monitoring the situation and working with Air New Zealand to smooth demand and ensure returnees can be safely housed in managed isolation facilities.
More than 26,400 people have been through managed isolation and quarantine since 26 March.