Health Minister David Clark won't be getting his job back in September if Labour is re-elected, the Prime Minister says.

Jacinda Ardern said last week she "had discussions" with Clark and how the primary focus should be the Government's response to Covid-19

Clark tendered his resignation to Ardern yesterday which was accepted.

This was the first time he offered his resignation since after his bike ride and trip to the beach during lockdown.

She hasn't "closed that door" for Clark being given any other portfolios after the election, but it wouldn't be health.

"I will leave that door open."

Ardern said they couldn't afford to lose one of their "key players" when he offered his resignation during the lockdown but now it was clear the response to Covid-19 was the priority and it was clear Clark in the role was a distraction.

New Zealand couldn't afford to have any distractions, Ardern said.

They had a "very frank" discussion in person last week, where they discussed "some issues" that were getting in the way.

"We need as a country, as a government, as a Cabinet to be completely focused on our Covid response."

Ardern said the ongoing response needed "really clear leadership" and Clark felt he couldn't do that.

"We had a discussion around what we needed to do to keep Covid as a priority ... it was his view that he needed to go."

"While Minister Clark made this decision it is one that I agree with."

Ardern said ultimately it was Clark's call and his judgment.

Chris Hipkins is standing in as Health Minister until the election when it will be re-assessed if they're re-elected.

Hipkins said he would sit down with the health team and work through the response to Covid-19.

As well there were "pressing challenges" in the portfolio, like Heather Simpson's review, capital investments which would "require constant supervision and nurturing".

He said he had a very good working relationship with health chief Ashley Bloomfield but they hadn't spoken this morning as had been "playing a bit of phone tag".

Hipkins said he felt Bloomfield had "thoroughly earned" his holiday next week and hoped he'd still take it, despite the change in ministers.

Hipkins doesn't have any experience in the health sector but said "I enjoy a good challenge" when asked if it was a portfolio he'd been eyeing.

Clark said it had been an "extraordinary privilege" and he had given it "my all".

But continuing was distracting from the Government's Covid response, he said.

He said he looked forward to having more time to serving his electorate of Dunedin North, and he intended to stand in the seat again in September.

He had already offered to resign over his beach excursion during the lockdown, which Ardern would have accepted were it not for the Covid-19.

He said the team had to come first and the Covid response was too important, so he had made the call to step aside.

With no community transmission and the focus now on the border measures, "it is appropriate for me to move on".

He thanked the frontline health workers and all Kiwis who made sacrifices to put New Zealand in a position to be the envy of the world.

"Now is the right time to hand over the reins."

Ardern said in a statement this morning that "David Clark contacted me yesterday to confirm his wish to resign as a Minister and I accepted that resignation".

"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," Ardern 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.

Clark under pressure

Clark had been under increasing pressure to step down, but he had been repeatedly backed by Prime Minister Jacinda Ardern, even though she said she would have sacked him over his lockdown breaches if she didn't need continuity in the health response to Covid-19.

Clark was demoted after driving his family 20km to a beach to go for a walk in the first weekend of the lockdown.

He had also gone mountain biking during the lockdown, though that was not as clear a breach of the rules as driving to the beach.

"At a time when we are asking New Zealanders to make historic sacrifices I've let the team down. I've been an idiot," Clark said of his beach excursion.

He also came under intense pressure over the bungles at the border in recent weeks, and was the subject of public criticism over video footage that went viral as he seemed to throw director general of health Ashley Bloomfield under the bus as Bloomfield was standing behind him.