Health Minister David Clark has resigned from the role, having narrowly avoided being sacked during lockdown.
He will remain as the Dunedin MP and will run at the next election.
Education Minister Chris Hipkins will take over as Health Minister until the election.
Dr Clark said his position in the role was a distraction for the Government during the pandemic.
Dr Clark had a number of issues during lockdown that normally would have seen him sacked then.
It comes after a string of issues during the Covid-19 pandemic, including his breaching of lockdown rules.
He said he took full responsibility for that and called Director-General of Health Dr Ashley Bloomfield an "exceptional" public servant.
"I’ve made the call it is best for me to stand aside."
The Health Minister continues to be questioned about issues with quarantine testing, but he is passing responsibility to his officials.
He said it was now appropriate for him to move on.
"It has been a privilege to serve in this role," he said.
Prime Minister Jacinda Ardern said she accepted Dr Clark's resignation yesterday.
"David has come to the conclusion his presence in the role is creating an unhelpful distraction from the Government’s ongoing response to Covid-19 and wider health reforms," she said.
"It’s essential our health leadership has the confidence of the New Zealand public. As David has said to me the needs of the team must come before him as an individual."
She said after his earlier breaches of lockdown rules that the only reason he wasn't sacked was the fact NZ was battling a health crisis and global pandemic.
David Clark moved between his new and old home during the coronavirus lockdown.
She appointed Mr Hipkins to Health Minister and would reassess the position after the election.
Labour MPs Grant Robertson and Kris Faafoi stood behind him as he delivered the news from Parliament.
Dr Clark faced a string of issues during the Covid-19 pandemic.
On April 3 during lockdown, Dr Clark apologised after going on a bike ride at a mountain bike park. Three days later, he apologised to the Prime Minister after taking a 20 kilometre drive to go for a beach walk.
Last week, he was criticised after pointing the blame for border blunders at Director of Health Ashley Bloomfield, while Dr Bloomfield was standing nearby.
Dr Clark was first elected as MP for Dunedin North in 2011, he was previously an analyst at Treasury and ran a residential college at Otago University.
He had been Health Minister since 2017.
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