Just one person was staying at Wellington's Grand Mercure MIQ facility earlier this week.
National's Chris Bishop called it "unbelievable" and a "massive slap in the face for the tens of thousands of Kiwis offshore who are desperately trying to come home".
A MIQ spokesperson said it was due to cohorting between groups of guests.
There was a week-long period between a group of 65 that left on October 21 and the 105 new returnees that arrived yesterday.
After the group of 65 left, the facility was closed for two to three days for cleaning.
"The Grand Mercure Managed Isolation Facility has 89 isolation rooms and 13 quarantine rooms. However, from May to early-October capacity was halved while maintenance work was carried out on the facility’s ventilation systems," the spokesperson said.
"During quieter periods, the on-site health team work remotely to support their nursing colleagues in Auckland."
Bishop said the news would "go down like a cup of warm sick".
"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."
The single guest had been involved in an emergency medical evacuation, a MIQ spokesperson said.
"International flight arrivals meant that there was a gap of a few days until a suitable flight arrived that could be transferred to Wellington in a single cohort."
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