"While the facts are in dispute, the report says an incident occurred. Meka Whaitiri continues to contest details of the incident, but there are elements which are agreed," Ardern told reporters.
She would not reveal further details of the report by Ministerial Services because it was an employment matter and to protect the privacy of the staff member involved.
But she said a version of the report would be publicly released.
Ardern would not be drawn on whether an assault took place, saying she was waiting for that report to be made available.
She had spoken to Whaitiri who had accepted her decision but still maintained her position. Ardern said she talked to her about providing support on staff management.
Whaitiri could not be reached for comment today.
Ardern said she still had confidence in Whaitiri as an MP and left the door open for her return to Cabinet.
"I like to, of course, leave openings for ministers to address the issues that been raised that have led them to lose their portfolios. I will do that for Meka as well."
Whaitiri holds the Māori electorate of Ikaroa-Rāwhiti, which stretches down the east coast of the North Island and Ardern said she would remain an MP.
"I have a view that the member works incredibly hard across Ikaroa-Rāwhiti, that she will continue to be able to fulfil those roles. However, based on what I have seen, I do not have confidence in her retaining her role as minister," Ardern said.
Whaitiri had held the portfolios of Customs, Associate Agriculture, Associate Crown Maori Relations, Associate Forestry and Associate Local Government.
Consumer Affairs Minister Kris Faafoi, who took over the Customs portfolio when Whaitiri was stood down, would keep it, Ardern said.
Whaitiri's associate minister responsibilities would revert to the lead ministers, and Ardern said there were no plans for a Cabinet reshuffle.
Ardern said Labour's Māori caucus, which had thrown its weight behind Whaitiri - the co-chair - when she was stood down, supported her decision and Whaitiri would remain as co-chair.
"I've been advised by colleagues in her caucus that they wish to still support her in that role," she said.
Māori caucus co-chair Willie Jackson declined to comment on the decision today.
National leader Simon Bridges said there were a trail of unanswered questions.
"Not only is the Prime Minister supporting someone who has shown no remorse but someone who denies anything happened," he said.
