More than half the rooms at Wellington's only MIQ facility were sitting empty over the New Year period.
MIQ's general operations manager Chris Scahill said the last cohort of international returnees before New Year arrived to the capital on December 29.
Wellington's Grand Mercure Hotel, located on The Terrace, had 92 isolations rooms and 13 quarantine rooms available on this day, when 44 passengers arrived off a single flight from overseas to go into 10 days isolation.
They took up 34 rooms, leaving 58 unoccupied over the New Year period, for the days following December 29.
Cohorting rules followed by MIQ meant people could not be added to the facility outside the two-day arrival window in which they filled rooms.
Information provided on the MIQ website says empty rooms are often a result of cohorting.
"While these rooms may be empty, they are actually allocated to a cohort and are therefore unavailable for use during that cohorting cycle," it states.
"On average, cohorting has reduced room availability by around 6 to 7 per cent."
MIQ acting deputy secretary Andrew Milne said flight schedules into Wellington played a "vital part" of the hotel's occupancy. While there are no direct international flights into the capital, groups of international returnees are transferred from Auckland to Wellington.
"If flights are cancelled or delayed at short notice, or passenger loads are low, this has a significant impact on occupancy, and more rooms are unoccupied.
"MIQ does not have any control over flight schedules or flight cancellations."
Milne said Wellington Airport was not set up to easily cater for red zone flights, and MIQ did not have access to its commercial terminal.
"However, we have been able to use the RNZAF's Rongotai terminal on the other side of the airfield for transfers from Auckland.
"This is a smaller facility and can be disrupted by other private flights."
There were also "compounding factors" such as availability of a charter plane and arrival time of incoming flights.
"For example, any mid-late evening international arrivals can't be transferred in time to get them to Wellington before the runway closes. It's logistically challenging."
Wellington Airport said last year it had never struggled to safely meet the capital's MIQ demand and could handle more red zone flights if necessary.
The Government made changes to the MIQ process late last year in light of the new Omicron variant, including increasing the length of stay to 10 days for all international arrivals.
Meanwhile nearly 11,000 people queued online last week for 1250 available MIQ spots – this lottery attracted three times as much interest as the previous one on December 16.
Scahill said the latest cohort of international returnees arrived at the Grand Mercure yesterday, which was 97 passengers occupying 61 rooms.
The capital is also down to one MIQ facility in 2022, with the last group of international arrivals leaving the Bay Plaza Hotel a week before Christmas.
In September the Ministry of Business Innovation and Employment revealed ventilation in the Bay Plaza Hotel, located in Oriental Bay, was not up to Delta-standard and the hotel would cease operating as a MIQ facility at the end of 2021.
Scahill confirmed this week the last international returnees left the Bay Plaza on December 18.
The facility would end its contract with MBIE this month, and is now preparing to re-open as a regular hotel in February.