"If a healthcare worker is unvaccinated, they can continue to see patients only if they are working 100 percent remotely or via telehealth.
"The Ministry had previously declined a request for a Temporary Significant Service Disruption Exemption for Dr Girouard to still practise while unvaccinated."
The offending occurred on December 2. At the time, the infringement fee was set at $300.
"Infringement fees for these offences were subsequently increased from $300 to $4000 shortly after the offence occurred," the ministry said.
On Monday, the Medical Council confirmed Girouard cannot practise medicine at all in New Zealand. Her entry on the Register was removed following her request and took effect on December 22.
Her anti-vax actions were the subject of a police investigation after a complaint from the New Zealand Medical Association. It is understood that investigation is ongoing.
The Medical Council told the Herald that Girouard was no longer listed as registered and able to practise in New Zealand.
"Council takes these matters very seriously and our concern is demonstrated by the publication of our recent guidance emphasising Council's view that there is no place for anti-vaccination messages in professional practice, nor any promotion of anti-vaccination claims including on social media and advertising by health practitioners," said council chairman Dr Curtis Walker.
"The council steps in as early as possible when a notification is made, or information comes to light to put in place any necessary arrangements to make sure patients are kept safe."
In the undercover Newshub expose the doctor boasted of using the certificate to get an exemption to keep working, saying it was easy, as her husband was her employer.
Her husband Michael, a director of the Girouard Centre, is also under investigation.
Anaesthesiologist-turned-weight loss expert Michael Girouard shares a similar anti-vax stance as his wife, appearing recently on a social media conspiracy site talking about his unvaccinated status before raising issues about the vaccine's safety.
Michael Girouard is not registered to practise in New Zealand as a medical doctor and the couple's Girouard Centre weight management and wellness website states that he isn't registered to work in New Zealand as a GP.
However, the Girouard Centre website says Michael Girouard is available for non-medical appointments at their Canterbury clinic.
In October Michael Girouard took part in an anti-vaccination online symposium and spoke for 45 minutes about complications connected with the vaccine.
He said he had not taken the vaccine, his stance guided by his pledge as a doctor to "do no harm".
The Ministry of Health says if a healthcare worker is unvaccinated, they could continue to see patients only if they were working 100 per cent remotely in a telehealth setting.
The Herald has approached Dr Michael Girouard and Dr Jonie Girouard for comment. They have yet to respond to requests.