Cabinet ministers Poto Williams and David Clark, both already demoted under Ms Ardern, and Pacific Peoples Minister Aupito William Sio will not contest the next election.
Three backbenchers will also exit - Jamie Strange, Marja Lubeck and Paul Eagle.
The ministers will keep their roles for the next month as Ms Ardern spends her summer break considering a portfolio reshuffle.
The prime minister denied any of the six were pushed.
"I've had conversations with each MP and minister," Ms Ardern said.
"They've each made their own call based on their personal circumstances which I both understand and respect.
"To each, I want to say thank you."
Ms Williams was sacked as police minister earlier this year when Ms Ardern cited a losing narrative on crime.
Dr Clark lost his job as health minister in 2020 after he was seen mountain biking in contravention of New Zealand's early lockdown rules.
Mr Eagle was expected to retire after he took leave to contest the Wellington mayoralty, finishing third in a Labour-friendly city.
The departures will create vacancies in electorates across the country, including Hamilton East, Christchurch East, Dunedin and the Wellington-based seat of Rongotai.
Labour faces an uphill battle to win next year's election, falling behind the centre-right opposition National party in the polls.
The next election is expected in late 2023.
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