Prime Minister Jacinda Ardern says she "agrees" with David Clark that he had become a "distraction" from the Government's COVID-19 response.
The Prime Minister accepted Dr Clark's resignation as Health Minister on Thursday and the role has now fallen into the hands of Education Minister Chris Hipkins until the election.
Ardern held a press conference on Thursday and said she had a "very open conversation" with Dr Clark about how to "put the COVID-19 response first".
She said Dr Clark had since "came to the conclusion" he could not continue in the role.
"Last week I had discussions with Dr Clark and we talked about how important the COVID response was and the need for that to be our primary focus as a Government, as a Cabinet and as ministers," Ardern said.
"He reached the conclusion his ongoing presence in the health role was causing too much distraction to the Government's ongoing response to COVID-19 - an assessment I agree with. He came to the very firm view that his ongoing role in this portfolio was going to get in the way of that response."
Ardern lauded Dr Clark for putting the interests of his team above his own.
"I want to thank him for his service. He delivered a lot in his three years as Health Minister and there are many things that he can be proud of."
She has appointed Chris Hipkins as Health Minister because as Education Minister he has experience with an operational ministry of significant scale, and also because of his role as Minister of State Services.
"Our COVID response is an all-of-Government response. Making sure that you have a good understanding and awareness of how to draw in the public sector as effectively as possible is one of the strengths that minister Hipkins has."
Ardern smiled when a reporter asked Hipkins if the health portfolio was something Hipkins had his eye on.
"Very few in Government eye up health."
Dr Clark came under fire recently after Newshub footage showed him pointing blamed at Director-General of Health Ashley Bloomfield for the Government's quarantine testing botch-up.
Dr Clark also faced backlash during the alert level 4 lockdown for breaching the rules by going mountain biking and driving 20km to the beach for a walk with his family when Kiwis weren't allowed to drive for recreation.
The Prime Minister said after the election she plans to "reassess who is best placed" to take the health portfolio forward, should Labour win.
Newshub also revealed he continued moving house during alert level 4 lockdown, shifting boxes when the rest of New Zealand was told they were not allowed.
The Prime Minister demoted Dr Clark to the bottom of her Cabinet rankings and stripped him of his Associate Finance portfolio, and said she would have sacked him "under normal conditions".
In the latest Newshub-Reid Research poll, voters were asked whether Dr Clark should remain Health Minister. More than half - 56.8 percent - said 'no', with only 35.7 percent saying 'yes'.
In Labour's recent reshuffle infectious disease expert Dr Ayesha Verrall - who rose to prominence during the COVID-19 crisis - appeared just one ranking below Dr Clark.
Dr Verrall has not ruled out ambitions for the health portfolio.