Managed Isolation and Quarantine (MIQ) head Brigadier Jim Bliss is unclear whether Grand Mercure and Grand Millennium hotels have upgraded ventilation systems with high-efficiency particulate absorbing (HEPA) filters.
It comes as an investigation begins into how Covid-19 was transmitted in those facilities.
Genome sequencing showed the virus spread between two returnees at the Grand Mercure, who arrived back on different flights, days apart.
At the Grand Millenium, a returnee, a cleaner and two security guards are in a single chain of transmission.
There are 224 isolating returnees across both hotels and once they all complete MIQ there will be a review of potential sources of spread at the facilities including the ventilation systems.
Bliss told Checkpoint risks presented by the ventilation systems had always been assessed by health experts as being very low.
"The risk to staff and returnees contracting Covid-19 within the facilities is low."
The Pullman Hotel in Auckland was the first isolation facility to close for a ventilation systems upgrade.
"When we did the Pullman review we also undertook to do a system-wide review of all of our facilities, and that started with a desktop review. As the opportunity allowed we'd conduct a physical review of each of our facilities.
"So the opportunity is now to do that physical review of the Grand Mercure and the Grand Millennium. So once we've had those remaining returnees depart on 21 and 27 April, we will undertake that physical review."
At the time, all MIQ facilities were promised HEPA filters.
He could not say whether or not the Grand Mercure and the Grand Millennium had upgraded ventilation systems. "I would have to go back and check."
He said both hotels had a ventilation facility which was appropriate to operate as a hotel.
Bliss said while physical contact or surface touching had known to spread Covid-19, "aerosol transmission is now seen as being, whilst unlikely, one of the more possible causes for transmission so we need to investigate that further, and fully".
The closure of the two facilities will mean 652 rooms that will be out of action - that's space for 900 returnees.
He said the reduction of the number of allocation spaces from the quarantine-free travel from Australia meant there was capacity in MIQ facilities and it would not be impinging on anyone's ability to return to New Zealand.
He could not say when the hotels would reopen as MIQ facilities.
"Part of the review is to determine what is the remediation plan, if any, that is required for each of those locations. The Pullman was to be [reopened] by the end of April and we're on track, or ahead of track to open the Pullman back up to full capacity, either later this week or next week."