Whaitiri, who is said to be difficult to work with, reportedly became involved in a heated exchange with a new staff member last week.
"What I'm balancing here is principles of natural justice," Ardern said.
"As soon as I found out about this issue I took action to make contact, of course, with the minister.
"She offered up to stand aside while this investigation takes place. That is the right thing to do. And once we have the report completed then I will make a decision on how to deal with it.
"It's only fair that we look into it properly first."
Ardern would not comment on reports Whaitiri "manhandled" a person out of her office.
Asked about training for ministers, she said: "We seek guidance, as any employer does, from those who work across those issues to make sure that we're always performing as the public would expect us to."
She said she had faith in her remaining ministers.
At a press conference in Auckland this afternoon, the Prime Minister was also asked about former US intelligence analyst Chelsea Manning after Immigration New Zealand announced that she would be allowed to apply for a visa to visit here for two speaking engagements.
Ardern said Mannings' views would be of interest to New Zealanders and people should be allowed to hear her speak.
Ardern declined to characterise Manning as either hero or villain for her actions in leaking hundreds of thousands of classified documents to Wikileaks, but said Immigration NZ would have made its decision based on the information it was given.
