The Ministry of Health initially recommended moving to the traffic light system only after 90 per cent of the adult population, 5 to 11 year-olds and vulnerable groups - including Maori and Pasifika - were fully vaccinated.
It also wanted national coverage of vaccinations would ideally be "equitably distributed", with a minimum of 85 per cent in any DHB area and a focus on coverage for vulnerable populations.
Doing so, the ministry said, would minimise hospitalisations and deaths while allowing as much social and economic activity as possible and retaining social licence.
The ministry's feedback is contained in a briefing to Prime Minister Jacinda Ardern from the Department of Prime Minister and Cabinet, which has been released today along with a tranche of other official documents.
The ministry added that the transition to the new system should only be made when the health system was ready, and at that stage - in early October - it wasn't there yet.
It also advised that the red setting would not be restrictive enough in some scenarios to contain the virus.
Meanwhile the independent advisory group chaired by epidemiologist Sir David Skegg told the Government that the new system would widen existing health inequities, particularly for Maori and Pasifika.
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That was because they were less vaccinated, more likely to live in crowded houses, and had higher rates of comorbidities and more barriers to accessing healthcare.
Skegg's group said "it was unclear why some measures were being proposed at different levels and not others.
The National Iwi Chair's Forum told the Government that 95 per cent of eligible Maori should be vaccinated before moving into the new system, the restrictions in the red setting needed to be stronger, and local communities should have the power to impose restrictions.
Eventually the Government decided to ditch its 90 per cent prerequisite for a 90 per cent target for each DHB region and moved the whole country into the new framework on December 3.
Earlier this week Covid-19 Response Minister Chris Hipkins revealed that concerns about pockets of low vaccination rates and active cases stopped the South Island, Wellington, and two regions from entering the traffic light system at green.
Director-general of health Ashley Bloomfield was also advised by his deputy Maree Roberts that Northland could start in orange, based on the area's case load and health system readiness, but the assessment committee eventually took a more cautious approach and recommended red for Northland and Auckland.
The Herald this week revealed public health officials at one stage wanted some regions to start the new response model at the least restrictive green setting.
The South Island, Wellington DHB areas, Hawkes Bay and MidCentral (between greater Wellington and Whanganui) were previously considered.
But some health officials also had concerns about areas with low vaccination rates and active Covid-19 cases, and so the green light was deemed too risky.
Cabinet decided to put Auckland, Northland, and several districts from Whanganui northeast to Gisborne in red, and everywhere else in orange.
Strong case for saliva testing, document shows
A briefing on April 14 to Hipkins on surveillance tests and tools called for alternative testing platforms and more consistent tests at the border.
The briefing from the DPMC (Department of the Prime Minister and Cabinet) said there was a strong case for adopting saliva testing as the main testing method.
"It would likely be of benefit to have experts on hand to provide advice in this fast-moving field," the briefing added.
The same April document said testing wastewater and air samples were probably less worthwhile than previously thought.
"There is a need for a rigorous process, given that New Zealand has now started Covid-19 vaccination rollout," the DPMC April briefing added.
"Surveillance and testing strategies will need to tie in closely with an agreed overarching goal for the response and how the situation will evolve, before and after maximum vaccination coverage is reached and border policies change."
Health staff 'tipping point'
A public health assessment on November 17 noted the pressure that testing labs were under, with only 49 per cent of tests being turned around within 24 hours.
Reducing testing for lower risk essential workers coming and going from Auckland was recommended to ease the pressure on testing labs.
This is despite a case in Canterbury having travelled to Auckland to attend a tangi in the last week.
Surge capacity for contact tracing had also been activated.
"The public health service is increasingly becoming stretched and is potentially reaching a tipping point where staff will be lost," the Minister of Health was told, as staff supported 5010 to isolate at home including 2238 cases," the Health Minsitry document, dated November 18, said.
Work was underway to change the way case investigation and contact management was done to make it more sustainable, but "the easing of workload is yet to be realised".
Shifting Auckland to step 3 of level 3 - which never eventuated - was of "little value" before moving to the traffic light system.
A Ministry of Health memo on October 14 discussed the possibility of "at least most" students being able to return to schools in level 3 areas in the week of October 25.
Ultimately only secondary school students in Years 11-13 returned on October 26, with the years one through 10 not returning until from November 17.
"Education is critical for young people's health and wellbeing and term 4 is particularly important for senior students sitting NCEA exams," the memo said.
"The impacts of education restrictions in Auckland are growing and consideration needs to be given to addressing these impacts."
Education in the classroom was "relatively low-risk", but interactions outside the classroom and in the community beyond school needed to be minimised.
Public health advice was that school could resumed once "appropriate precautions" were in place, covering IPC procedures, use of masks, and avoiding large indoor gatherings such as assemblies.
"We will provide further advice this week on whether (at least most) schools across the Auckland metro region might open safely the week of 25 October," the memo said.