Jacinda Ardern says Kiwis missing out on quarantine spaces in managed isolation is "sadly the reality" as the busy Christmas and summer periods draw closer.
Kiwis complained the nearly-full facilities had ruined their Christmas plans after thousands of New Zealanders booked out the system.
The Prime Minister said on Monday the finite number of rooms available meant some people would miss out.
"This is sadly the reality of any booking system, where in the short term there is greater demand than there is supply of spaces," she told reporters.
"But we can't simply turn on more places. Every new facility requires additional health staff, additional military personnel, police, and security presence. Our borders remain our first line of defence during this pandemic, and it's important that we manage those facilities and the return of New Zealanders safely."
It is compulsory for returning New Zealanders to secure their spot in the Managed Isolation Allocation System (MIAS). Everyone arriving in the country has to show a voucher to airlines to board their flight from their country of origin or have a special exemption from using the system.
Ardern said the booking system holds places for a short time while the person goes and books an actual flight, meaning rooms are held and then released often.
"For example, on a single day in December, there were more than 300 vouchers returned to the system for this reason. This re-release ensures these rooms don't go to waste," she said.
"So if you're someone with a voucher that won't be using it, that you've reserved a space but have found an alternate booking on a flight or changed your mind, please make sure you cancel your booking as soon as possible so that someone else can use that space."
Head of managed isolation and quarantine Air Commodore Darryn Webb said in a statement if, for example, someone's flight is cancelled and they don't cancel their managed isolation voucher, their space won't be allocated to someone else and it "goes to waste".
Ardern said she encourages people who are trying to get a voucher to keep checking for the release of rooms.
"Once we are through this busy spell that is the summer and Christmas period, I do anticipate supply and demand will be more evenly matched," she said.
Webb said 100 extra rooms had been made available from December 13 to 23. These are available now and will be released on a first-in, first-served basis.