People returning to New Zealand at about the same time will now be taken to the same managed isolation hotels.
The so-called enhanced cohorting system will mean people arriving in New Zealand over a 96-hour period will be taken to the same MIQ facilities.
Once they are full, or the 96-hour period is over, they will lock down for a 14-day cycle, with no more returnees allowed until the last of the cohort has left and the facilities have been cleaned.
Covid-19 Response Minister Chris Hipkins said the changes have been made because more rooms have been freed up with the opening of the trans-Tasman bubble.
"This will ensure returnees will be in the same facility as others who have arrived at about the same time, and importantly, will keep those who have just arrived apart from those who are coming to the end of their stay," he said.
The Pullman Hotel will be the first MIQ facility to receive cohorted arrivals, starting tomorrow.
The new system will be fully rolled out by mid-May.
The emptying process to transition to enhanced cohorting has already started, with five facilities no longer receiving new returnees to prepare them to receive a cohort of arrivals.
Infectious diseases physician Professor Kurt Krause, who teaches biochemistry at the University of Otago, told Checkpoint the move was a clever compromise.
"We know we have New Zealand citizens overseas and we can't stop them from coming back indefinitely, so I have to say I think it is actually pretty clever because it's cohorting the group of people who have arrived at the same time together.
"It minimises the cross-talk from them to other people who they might encounter who may be leaving and coming in constantly during their stay and they kind of leave together. So I think it is a clever compromise solution to what is a really difficult problem. The alternative is we just close the doors completely."
He said grouping only people from high-risk countries together would be a logistical nightmare. Krause said it would be better to instead put all people coming into the country on notice, immediately letting them know that they are at risk and that they should do everything possible to avoid infection, including mask-wearing and social distancing.
Special purpose MIQ facilities will not be included in cohorting. This includes the Jet Park quarantine facility and other facilities used for special groups such as refugees, unaccompanied minors, air and maritime crew and people with complex medical needs.