Clark first came under fire during the pandemic when it was revealed he took a trip to a beach with his family in the first week of level 4 lockdown.
David Clark announced his resignation on Thursday, saying his presence in cabinet was a "distraction" for the government.
The Prime Minister said in a statement that "David Clark contacted me yesterday to confirm his wish to resign as a Minister and I accepted that resignation".
Speaking at Parliament on Thursday morning, Clark said while he had given his all in the challenging health portfolio, it had become clear that his continued presence in the role was serving as a distraction from the Government's pandemic response.
Mr Clark said he meant to remain in the Parliament as a lower-ranking MP.
Calls for Clark's resignation have grown louder, with political commentators saying he has repeatedly proven himself a liability and had begun to tarnish the government's success in eliminating the virus.
He suffered a further PR reversal last week when footage of his stating breaches of Covid-19 quarantine regulations were an operational rather than a ministerial matter - which showed a seemingly crestfallen director-general of health Ashley Bloomfield in the background - was widely distributed on social media.
Mr Bloomfield, who was standing behind Mr Clark while he spoke, appeared stung by the criticism as he frowned and looked away in a video captured by local outlet Newshub and viewed tens of thousands of times.
Many individuals have been angered by Clark's phrases, and a Twitter marketing campaign dubbed "Blooms for Bloomfield" was launched to purchase flowers for Bloomfield.
That was the latest in a series of missteps by Mr Clark.
In April, he was stripped of a few of his obligations after defying the nation's strict lockdown measures.
"Whilst Minister Clark made this decision, it is one I agree with".
The Dunedin based MP also admitted to a second breach, after driving to a mountain biking track during lockdown.
NZ Prime MInister Jacinda Ardern has accepted Dr Clark's resignation.
Prime Minister Jacinda Ardern said at the time she normally would have fired him, but the country could not afford massive disruption in its health sector while it was fighting the virus.
"David Clark has not delivered in his role as Health Minister and there is no question he had to go".
In April, Ms Ardern instead demoted him but retained Dr Clark as Health Minister as a change in the midst of a health crisis would be too disruptive. "As David has mentioned to me, the wants of the workforce should come earlier than him as a person".
Ms Ardern has appointed Education Minister Chris Hipkins to temporarily take over the role.
The transfer comes lower than three months earlier than New Zealanders vote in a normal election.
Ms Ardern, who leads the liberal Labour Party, saw her popularity soar during the early stages of the virus response, although recent opinion polls indicate the conservative National Party, under new leader Todd Muller, is making inroads into Labour's lead.
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All parking facilities at state beaches in Southern California and the Bay Area will also be closed for the upcoming weekend. Tables are marked with X's for social distancing in the outdoor dining area of a restaurant in Los Angeles , Wednesday.
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