There has been just one person staying in Wellington's Grand Mercure managed isolation hotel in the past week, leaving more than 100 rooms typically used by returning Kiwis empty.
Managed Isolation and Quarantine confirmed the hotel had a single guest between October 21-28.
That left 88 isolation rooms and 13 quarantine rooms sitting empty in the hotel, media outlet Stuff said.
It said it also understood up to 50 staff remained working in the past week and that solitary guest arrived on a private plane following a family issue in New Zealand.
"Other guests have not been staying at this facility to maintain the cohorting system between incoming and arriving guests," MIQ said in a statement.
"The last cohort of 65 returnees left on October 21. The next cohort of 105 returnees [was] due to arrive at the facility [on] October 28."
The cohorting - or group intake - system is designed to reduce the chances of Covid spreading among guests within an isolation facility, the government said.
It works by having people arriving in New Zealand within a four day window of each other being moved into the same managed isolation facility.
"Returnees arriving in New Zealand over a 96-hour window are delivered to MIQ facilities until they are full or the 96-hour period is over," the MIQ website says.
"The facilities then close their doors until the end of the cohorting cycle, with no additional returnees allowed in until after the last of the cohort have completed their stay and the facilities have been cleaned."
Cohorting cycles can take between 18-20 days.
This is made up of 14 days to cover the Covid isolation period, plus four extra days for late arrivals to also complete their isolation and then an additional 1-2 days to clean the hotel.
The system does, however, mean that up to 15 per cent of the nation's managed isolation rooms can sit empty at any one time.
National's Covid-19 spokesman Chris Bishop called news of the virtually empty hotel "unbelievable".
"This is a massive slap in the face for the tens of thousands of Kiwis offshore who are desperately trying to come home," he said.
"While stranded Kiwis have been logging in and spending hours sitting at a computer screen in the MIQ virtual lobby and lodging desperate emergency allocation requests, almost an entire hotel stood empty."
It comes as the Government has been unable to meet demand for managed isolation rooms from returning Kiwis wanting to come back into the country from overseas in the lead up to Christmas.
Its new virtual lobby room booking system has regularly had tens of thousands of Kiwis competing for one of about 2000-3000 MIQ rooms.
"This latest debacle piles further inequity on top of the already inequitable system where fully vaccinated travellers go into MIQ for 14 days while over 200 people with Covid-19 isolate at home in the community," Bishop said.
"Fully vaccinated travellers with negative pre-departure tests present negligible risk to New Zealand, as data I revealed last week shows.
The Government did, however, announce yesterday that arrivals from several South Pacific countries will be able to enter New Zealand without MIQ requirements from November 8.
For other arrivals, the time spent in MIQ will be shortened and followed by a period of isolation at home.
The option of self-isolation at home will be made available to increasing numbers of fully vaccinated travellers in the first quarter of 2022.