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Dr Jonie Girouard, who runs a weight-loss clinic in Kaiapoi in Canterbury, has been offering a potentially illegal alternative option for people who do not want to get vaccinated.
The Ministry of Health said Dr Girouard's request for a Temporary Significant Service Disruption Exemption has been declined.
"It is critical for staff working in the health and disability sector to be vaccinated because they are caring for people who are at increased risk of severe illness from Covid-19," the Ministry said in a statement.
Unvaccinated healthcare workers can continue to see patients only if they are working 100 per cent remotely.
The ministry also confirmed it was "continuing to investigate this matter".
The police have also confirmed to Newshub they have launched an investigation into Girouard.
It comes as the New Zealand Medical Council confirms it has received a notification about Dr Girouard and is now considering how best to keep the public safe.
Recordings taken during a Newshub undercover operation showed Girouard issuing medical certificate exemptions to the vaccine to people who did not fit the exemptions criteria.
Her Kaiapoi waiting room is full and people are told they don't have to wear a mask if they don't want to.
"I understand everyone is here because they're concerned about the mandates and not sure how to negotiate that," she told those in the waiting room.
"You're here because you're not crazy about being vaccinated. Great, okay you are in the right spot."
Earlier today, Prime Minister Jacinda Ardern confirmed investigations were under way into the actions of Girouard.
Ardern said the doctor's actions were dangerous, and officials were making sure this would not happen again.
"I think everybody would be disappointed and upset to see a health professional undertaking activity such as this that puts people at risk."
She confirmed that officials in the Health Ministry were now looking at it.
"I do want to give some reassurance here - this appears to be the actions of some individuals here and we will be looking at ways of ensuring it cannot be replicated.
"If a medical professional is not vaccinated, they should not be operating."
Medical council chair Dr Curtis Walker said the council was aware of concerns raised about Girouard.
"Council is considering these concerns in terms of our primary role of protecting the health and safety of New Zealanders," he said.
The New Zealand Medical Council said there were a number of options available to the medical council if a doctor did not comply with standards including suspension or placing conditions on a doctor's practice to protect the public from harm.
Throughout the recordings, she openly discusses her view on the Covid-19 vaccine.
"I mean really this is horrible, horrible medicine."
Listening from a car outside the clinic, Newshub reporter Patrick Gower heard Girouard talk explicitly about how to negotiate with an employer about not being vaccinated.
"What we're trying to do is give a medical certificate saying that you've been assessed and it is not appropriate for you to receive the current vaccine," Girouard tells the waiting room.
During the recording, she also says one of her certificates has been used to evade international border control.