Justice Minister Paul Goldsmith says he has been aware of complaints made about the Human Rights Commission chief commissioner for a "couple of weeks".
Stephen Rainbow is being investigated by Kristy McDonald KC over concerns raised about his conduct.
Goldsmith said he would not comment on the nature of the complaints made about Rainbow's behaviour and the purpose of the investigation was to see whether the complaints met the "threshold for action".
He said the complaints were made over the last "few weeks and months" but he did not have an "exact date".
"I became aware of it a couple of weeks ago and the Human Rights Commission is a highly independent role, and there's clear procedures in place. I've taken advice, and we're having an investigation."
Goldsmith said he was disappointed that "we have to be doing such a thing, but it's an appropriate plan we've got in place".
The High Court ruled in December that Goldsmith appointed Rainbow unlawfully, finding he was not part of the initial shortlist of candidates, and Goldsmith requested that he be added in place of other candidates.
The panel in charge of assessing the candidates said it did not recommend appointing Rainbow, noting his lack of legal experience, but Goldsmith appointed him anyway.
Asked if he regretted appointing Rainbow, Goldsmith said he stood by it.
"No, I've made the appointment, stand by that appointment. This has come up, and we're dealing with it."
Goldsmith said he did not yet have the ability to suspend Rainbow, but he had confidence in the process.
Rainbow was appointed in 2024 prompting concern from some because of his staunch pro-Israel views and previous comments about "a trans agenda".
At the time Goldsmith said he expected Rainbow to be "very careful" in his public commentary.
Rainbow defended his appointment, saying he was committed to continuing the commission's work protecting the rights of trans people.

