Government Minister Meka Whaitiri will stand aside from her portfolios while an investigation is carried out into a staffing matter in her office.

Prime Minister Jacinda Ardern said she had accepted Whaitiri's offer to stand aside while the investigation was done.

While the matter, which has not been disclosed, was being investigated, Kris Faafoi would act as Customs Minister.

Whaitiri's Associate Minister responsibilities in Agriculture, Local Government and Crown/Māori Relations would revert to the lead portfolio ministers.

"Meka Whaitiri has told me she will be fully co-operating with the investigation, which will be thorough and conducted as quickly as possible," Ardern said in a statement.

Ardern and Whaitiri, who is a Minister outside Cabinet, said they would not comment further, citing privacy reasons, while the investigation was carried out by Ministerial Services.

Barry Soper told Mike Yardley that there are allegations, currently unproven, that Whaitiri had physically assaulted a staff member, and that is what is being investigated.

Soper says that Whaitiri has had a high staff turnover since she became a Minister in October, with at least five staff members leaving since then. 

Labour MP Kris Faafoi's been asked to step into the breach, and take up the Customs portfolio.

He told Mike Yardley he's happy to take the extra workload, but he won't comment on the alleged offending until the investigation's over

"I probably know as much as you in terms of what's going on. I think Mika has done the right thing in offering to stand aside and let that process do its thing."

Whaitiri was elected to Parliament in 2013 in a byelection in the Māori seat of Ikaroa-Rāwhiti, succeeding her former boss Labour's Parekura Horomia.

It is the second Labour Government Minister within a week to fall, with Clare Curran demoted from Cabinet and losing two portfolios last Friday over her mishandling of a meeting with entrepreneur Derek Handley.

It was strike two for Curran after she failed to disclose a late-night Beehive meeting with Handley over the chief technology officer role.

Curran did not diary the meeting and no staff were present. She also failed to mention the meeting in response to written questions.