While the assumption has been that the complaint centred on an altercation at Parliament, it is understood it relates to the Gisborne visit.
Te Runanga Ngati Porou chief executive Herewini Te Koha said he could shed no light on what had happened and he had not heard about incident.
Whaitiri will be absent from Parliament this week and possibly next week too, working from electorate offices.
Her electorate, Ikaroa-Rāwhiti, stretches down the east coast of the North Island from East Cape to Wellington and she has offices in Gisborne, Hastings and Wainuiomata.
She will continue to be paid a ministerial salary which Ardern said was usual practice when people are subject to an investigation.
"Her role continues on as a Member of Parliament whether she's in Wellington or in her home constituency," Ardern told reporters today.
Whaitiri held the portfolios of Customs, Associate Agriculture, Associate Crown Maori Relations, Associate Forestry and Associate Local Government.
Ardern expected the investigation to take weeks rather than days but hoped it was done as quickly as possible.
Ardern said it was appropriate for Whaitiri to remain co-chairwoman of Labour's Māori caucus.
"Yes, we're making sure this process happens as quickly as possible. She's stood aside from ministerial portfolios. All of her other roles remain for the time of the investigation."
Labour Māori caucus co-chairman Willie Jackson said at the weekend that it was appropriate for Whaitiri to remain co-chairwoman of the Māori caucus.
"In this country we go through certain processes, and she has to go through a process. She's still a member of Parliament," Jackson told Newshub Nation.
"What we believe in is justice, and I won't be commenting on the process. But she is still the MP for Ikaroa-Rāwhiti. She is still the co-chair, along with myself, for the Māori caucus.
"And I think all New Zealanders would agree there has got to be an investigation and a process to go through before we try to shut Meka Whaitiri down."
But Labour MP Peeni Henare told Maori TV's Te Kāea it offered an opportunity for others in the Māori caucus.
"We have a pool of options in our party," Henare said.
"For example, Willow-Jean Prime and Kiritapu Allan, who would make excellent ministers. There's plenty who could do the job and this could be an opportunity for them."