The Ministry said Dr Macdonald has deregistered with the New Zealand Medical Council, meaning he is no longer able to practice as a medical practitioner in New Zealand.
The Medical Council of New Zealand (MCNZ) confirmed Dr Macdonald's deregistration took effect on January 25 at his own request.
"Council can confirm that Dr Phil Macdonald is no longer registered with the New Zealand Medical Council and is no longer able to practice as a medical practitioner in New Zealand," MCNZ chairman Dr Curtis Walker said.
"A doctor is not able to deregister if they have disciplinary or criminal actions pending ... and deregistration does not prevent the council considering disciplinary action that took place while a doctor was registered.
"All matters concerning the investigation and enforcement of the practice of doctors while unvaccinated or not registered with the Medical Council sits with the Ministry of Health.
"The Medical Council thanks the thousands of doctors who are contributing to New Zealand's pandemic response."
Hawke's Bay Today has contacted Dr Macdonald for comment through his practice in Napier.
A blurb on the Napier Eye Ophthalmology website stated Dr Macdonald specialises in cataracts and he has speciality training in eyelid surgery.
He has been practicing in Hawke's Bay for over 15 years.
The Hawke's Bay District Health Board declined to comment.
If anyone has been treated by Dr Macdonald since January 26, they are asked to email the Ministry of Health at info@health.govt.nz or phone 0800 855 066.
The Ministry of Health has also issued two fines to Dr Deepak Gupta, a Dunedin eye surgeon. Dr Gupta has also deregistered.
CLARIFICATION
An earlier version of this story stated Dr Macdonald had been deregistered for seeing patients while he was unvaccinated.
To clarify, the MoH says Dr Macdonald has deregistered with the New Zealand Medical Council meaning he is no longer able to practice as a medical practitioner in New Zealand.