Newshub can reveal the Government didn't have anyone analysing the data it was collecting on border worker testing until two weeks ago.
The testing register was also only established in February - six months after the Government made it mandatory for staff at isolation facilities to be regularly tested.
Data teams are in their second week of analysing the register, which is critical to understanding the testing rates of a workforce at the highest risk of contracting COVID-19.
Disease modellers are disappointed over the delay.
"I think we would have expected it would have been set up by now," says Professor Michael Plank from Canterbury University School of Mathematics and Statistics.
"Mandatory testing was brought in around September last year, so you would expect that we are collecting the data because if you don't have the data, you're really flying blind."
Auckland University Physics Professor Shaun Hendy agreed.
"Those teams should have been in place right from the start, watching as that data came in and making sure that data was being used."
The Ministry of Business Innovation and Employment (MBIE), who is in charge of Managed Isolation and Quarantine (MIQ), told Newshub: "The Ministry of Health’s testing register went live in February, and shortly after we began recruiting a team of data analysts. This team has been in place at MBIE since the beginning of the month."
National's COVID-19 Response spokesperson Chris Bishop said the delay is "incompetent".
"It turns out they've only been analysing the data on the register since the beginning of this month. It's dangerous, it's very worrying, and frankly, it's incompetent."
ACT Party leader David Seymour branded it a "catastrophic failure".
"To find that [the systems] have only been put in place in April 2021 is a catastrophic failure of the Government's response."
Last Friday, Newshub revealed the Government was in the dark about how many workers had missed their tests.
Since then, an investigation has been established - but not before a COVID-positive 24-year-old security guard, referred to as Case B, was blamed for missing tests.
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Prime Minister Jacinda Ardern and COVID-19 Response Minister Chris Hipkins both claimed the guard had lied about their testing record.
"The individual is lying to their employer," Ardern said on Wednesday, despite the investigation still being underway.
Hipkins followed with a similar tone on Thursday: "Look, it's clear that the worker had been supplying information to their employer saying they had been tested, and they had not been tested."
The individual's employer First Security said all its guards are "required to sign declarations that they are up-to-date with the COVID-19 testing requirements". It also said it has "current proof of up-to-date COVID-19 testing from all guards working at MIQ facilities".
MIQ joint head Megan Main told the AM Show on Thursday the employer's testing information didn't match the Ministry of Health's data, which is how they found out the worker hadn't been tested.
She wasn't sure if the worker had provided actual proof of testing to his employer, or had just lied about it.
Regular fortnightly testing has been a legal requirement since September last year and from April 27, all border employers will be required to use a centralised register.
First Security told Newshub it joined the Government's register as soon as it could, and "the system did not flag the guard as non-compliant until March 26".
Bishop says the Government needs to take the blame: "The Government can lash out and blame whoever they like - ultimately this is on them."
Hendy thinks had the system been running sooner, we could have avoided the lockdown in February.
"I think this is something that would have been good to have in place late last year. We might have been able to avoid the Valentines Day alert level 3 period."
Despite varying figures being offered up publicly this week, Hipkins has confirmed 74 MIQ workers didn't get tested at all last week despite being required to. A further 450 missed scheduled tests, but then got them a few days later.
But that's just out of the 4000-odd MIQ workers. As for the roughly 15,000 staffers across airports, the Ministry for Primary Industries and ports, the rate of compliance is unknown.