Dr Ashley Bloomfield says keeping people in their rooms for their whole stay in managed isolation doesn't completely remove the risk of COVID-19 spreading.
Health officials are investigating whether changes are needed after managed isolation guests shared a bus with a COVID-19 case.
The Ministry of Health is investigating whether the bus case caught COVID from another guest at the Grand Mercure Hotel after genomic sequencing linked the pair.
During a press conference on Friday, head of MIQ Brigadier Jim Bliss said bus trips from hotels to exercise areas had been halted for 24 hours while the case was investigated.
Bliss said there are four MIQ facilities that use buses, the rest have onsite exercise areas.
The positive case took a bus on March 19 and 21. There are nine close contacts from the trip - all of whom have tested negative. There are 14 close contacts from the March 21 trip who have had their stays extended by a fortnight. Dr Bloomfield said despite the busses being halted, guests won't be confined to their rooms like in Australia.
"We are picking up the vast majority of our injections at day zero testing and as part of that protocol all returnees remain in their rooms until the result of that testing is available."
"Just two weeks ago… in the same weekend, Australia had cases in both Brisbane and in Sydney. Related in Brisbane to a health worker, who had been in a managed isolation facility providing care and, in Sydney, a security officer.
"Confining people to their rooms for 14 days does not completely take away the risk associated with infection inside facilities."
Bliss added that being stuck in a room for two weeks can have mental health ramifications.
"Being able to exercise is an important aspect of mental health and well-being,” he said.
There were three new COVID-19 cases in managed isolation today and none in the community.
All three of the new cases arrived from India via the United Arab Emirates, though on different days. Their detection takes the total number of active cases in New Zealand to 74, with the confirmed cases recorded since the beginning of the outbreak now standing at 2123.