The Ministry of Health estimates more than 70,000 people who identify as Māori in Census-based population estimates are not recorded with this ethnicity in the internal database it uses to measure vaccination rollout equity.
Māori data and health experts say the discrepancy is "highly concerning" and makes a mockery of Government claims it is prioritising and anywhere achieving equity for vulnerable groups.
It comes amid a huge push to make the rollout more equitable by increasing vaccine availability particularly for Māori, with the rate compared to non-Māori dropping week on week.
To date the rollout has implicitly prioritised European/Other ethnicity. This is due to the rollout's age distribution and the fact they are disproportionately represented in the essential worker groups, despite research showing Māori and Pasifika are much more vulnerable to the virus at lower ages.
Consequently at the beginning of August, according to the Ministry's data, Māori as a population were fully vaccinated at a rate of 69 per cent compared to the non-Māori rate.
As of Tuesday it had dropped to 62 per cent of the non-Māori rate. This is despite the rollout opening up to younger age groups, which the Government assured the public would see equity increase.
There is inequity spread across every age bracket, with rates close to equal in some older groups but dropping to about half for those aged under 40.
Meanwhile, Herald analysis of the datasets being used has revealed the true rates for Māori could be even lower.
Until early August the Ministry had not released vaccination rates by ethnicity, instead just providing raw vaccination numbers.
Data describing vaccine rates for different population cohorts was finally released several weeks before the most recent outbreak.
This revealed the Ministry was not using Census population data as the basis for its population estimates. Instead, officials relied on their internal Health Service Utilisation (HSU) database.
This dataset, used only by the Ministry of Health, includes all individuals enrolled with a primary health organisation (PHO), or who have used other health services such as hospital admissions, the emergency department, or filled a prescription, during a calendar year.
However, comparing the current Māori population projections from the 2018 Census to the HSU database for the eligible vaccination rollout (12 and over), there are just over 12 per cent - 73,889 - fewer Māori. The group classed as European/Other is larger in the HSU database than in the Census estimates by nearly the same amount.
Looking at the dataset overall there are about 80,000 fewer people in the HSU compared to Census projections.
The Ministry says it is certain those missing people are evenly spread across ethnic groups, which means the main Māori population difference is likely subsumed into the European/Other, meaning there is no way of knowing the true rates of vaccination by ethnic group.
National Māori Pandemic Group member Dr Donna Cormack, of Kai Tahu and Kāti Mamoe, said she had long been raising concerns about the Ministry's population and ethnicity data set.
There were problems with the way it was recorded including tech issues and a lack of standardisation across the country.
Her research has found in some cases ethnicity was not even asked by clinicians but assumed. In other cases Māori could also be identifying as Pākehā due to racism in the health system, she said.
Another issue was that just 85 per cent of Māori were registered with a primary health organisation, compared to 94 per cent of the New Zealand population overall.
"There are major issues with their dataset," said Cormack, a senior lecturer at the University of Auckland.
"The problem is it makes it harder for researchers and communities to know what is going on, especially when they only release it weeks before a major outbreak hits."
As of Tuesday, Pasifika were also under-represented in the rollout, at a rate of 81 per non-Pasifika for a single dose, and 84 per cent for two doses.
This has raised major concerns from health leaders, with nearly three-quarters of the 821 cases in the latest outbreak identifying as Pasifika.
Inequity also varies greatly across the country, with Northland and Lakes district health boards, both which have high Māori populations, at the bottom end where the rate is almost 50 per cent behind.
Meanwhile Capital and Coast DHB is the most-near equity at just 16 per cent behind on both doses for Māori, and at or above equity for Pasifika.
At a population level, Māori on average die seven years younger than non-Māori, due to health inequities.
Modelling on the initial Covid variant found at a population level Māori could be twice as likely to die from the virus, and were more likely to catch it.
Further research released in July, by Te Pūnaha Matatini, found Māori and Pasifika were twice as likely as Asian people and New Zealand European/Other to be hospitalised from Covid-19.
Even after factoring in underlying health conditions, Māori and Pasifika were at the same risk of hospitalisation 20 and 25 years earlier respectively than Pākehā.
Ahead of the vaccine rollout Cabinet was advised to give higher vaccine priority to Māori and Pacific peoples aged 50-64, reflecting these inequities.
This also reflected the younger age distribution, however Cabinet decided against the advice.
Cormack said the low rates consequently were not for a lack of desire, rather the younger age distribution and lack of access to the vaccine.
Extra Māori-led clinics and even drive-thru vaccination centres in the past few weeks in key areas were seeing enormous demand, raising questions as to why it had not occurred sooner.
"About 70 per cent of our population is aged below 50, so it was always going to disadvantage Māori overall," Cormack said.
"It is frustrating when we hear things like low uptake when it is about access. Until recently a huge proportion of the Māori population was not even eligible. It is inequity by design."
The amount who have received a single dose has increased slightly over the past month, from 40 per cent behind to now 37 per cent behind the non-Māori rate, indicating these new initiatives could be having an effect.
Cormack said rather than rely on a dataset known to have flaws, the Ministry should have used the Census data, along with having people record their ethnicity when registering for a vaccination.
The data issues for Māori was "double inequity", she said.
"They developed a programme that was going to be inequitable, it has nothing to do with communities not turning up."
The Ministry confirmed to the Herald there was about a 12 per cent difference in Māori populations in the dataset it used compared to the Census projections.
Group manager equity for the Covid-19 vaccination programme Jason Moses said they did not know exactly why the difference existed, nor had they conducted any research to determine why.
The Ministry did not answer questions from the Herald nor grant any interviews as to whether it thought the discrepancy was concerning.
In a statement, Moses said the HSU data was more appropriate as it was based on health data, and would provide better information in areas where uptake was low.
"We do acknowledge that the use of HSU data has some limitations, with a small number of people potentially not included because they have had no interaction with the health system in a given year.
"However, our analysis shows that people who identified in the Census as Māori are not more likely to be missing from the HSU than people of European ethnicity.
"We have not undertaken any research into the reasons behind why people might self-identify their ethnicity differently to Government agencies, so couldn't comment on why this might occur.
"We are looking to update ethnicity detail for some people in some vaccination sites. We encourage people to update their ethnicity details if they believe the information we hold may be incorrect."