The Prime Minister hopes to avoid "arbitrary" capacity caps on flights similar to rules imposed in New South Wales, which is why the Government worked with Air New Zealand to halt ticket sales for three weeks.
Air New Zealand is putting "a temporary hold on new bookings" to ease the pressure on the Government's managed isolation facilities which are currently housing nearly 6000 returnees - but it's not as strict as across the Tasman.
The Australian state of New South Wales has limited the number of people per flight to 50 and allowing only 450 per day at Sydney Airport due to "significant pressure" on quarantine capacity and the suspension of international flights into Melbourne.
Jacinda Ardern said New Zealand is not alone in experiencing issues with the number of people returning home, which is why it was necessary to work with Air New Zealand to temporarily limit the number of ticket sales.
"I wouldn't call it a drastic step. When we look at the likes of New South Wales, they've put a hard cap - no flight any more than 50 passengers in a total of 450 per day. We, this week, will be managing more than that," she said on Tuesday.
"What we're seeing is an increasing number of New Zealanders continuing to put pressure on the system. We need to make sure that the well-managed facilities and operations that we have now we can maintain.
"We have people showing up at airports and by the time they close the doors, that's when we'll get a heads up that we have an extra hundred people coming that weren't planned for."
Megan Woods, the minister in charge of the Government's managed isolation facilities, said 98 transit passengers out of Hong Kong arrived on Saturday that were not scheduled for.
"This is a way that we can make sure we have managed numbers without using something that is considered too arbitrary," Ardern said, when asked if the Government would consider a cap similar to New South Wales.
"I think it makes complete sense that we work with the airlines. They've been fantastic to work with; we've come to a solution that is workable for them and workable for us."
Ardern insisted it has nothing to do with the Government's ability to manage the facilities.
"When you compare the number of New Zealanders coming home to even a few months ago we've had a significant increase. We are still managing to grow our capacity at a significant rate but we want to do it safely," she said.
"At the moment we are still expecting more New Zealanders coming in than New South Wales are accepting there. We have continued to grow but we just want to make sure we do it safely."
Health Minister Chris Hipkins said the Government is considering a booking system for the facilities.
"One of the things we're looking at is whether there should be a booking system so that people are booking their position in managed isolation before they board the flight back to New Zealand, so that we can better forecast when people are arriving and we can be prepared to accommodate them when they get here."
He said the Government understands that returnees are often returning from difficult situations and they are being given mental health support.
"We understand that being in managed isolation can be stressful for people and we also understand that people coming back to New Zealand may now have an increased need for support. They may be returning from stressful situations overseas or they may have had difficulty getting home."
Two new cases of COVID-19 were reported in New Zealand on Tuesday both in managed isolation facilities.
There continue to be no cases of the coronavirus in the community and it has been 67 days since a local case from an unknown source.