Chris Hipkins says Nanaia Mahuta's Cabinet colleagues left her alone for too long to defend Three Waters.
The Prime Minister told The Hui presenter Julian Wilcox other voices from the Government should have been in the conversation about the controversial legislation.
"I think if I reflect critically on that period, we probably left Nanaia Mahuta out on her own defending the Three Waters reform program and the co-governance debate by herself for longer than we should have," Hipkins said.
"I actually think Nanaia bore the brunt of that [debate]. It was very unfair. It became very personalised to her."
Hipkins said it was one of the reasons he took the Local Government portfolio off Mahuta in his first Cabinet reshuffle.
"I wasn't willing to allow that to continue... I think she deserved better than that."
He added many people who oppose Three Waters don't understand the water infrastructure changes.
Instead, the Prime Minister said they've "just heard the dog whistle racism that's associated with it".
Referring to the 2004 controversy surrounding the foreshore and seabed legislation, Hipkins said Aotearoa has "got to try to avoid that kind of potential to divide New Zealanders".
Wilcox said Māori were ready to go with Three Waters and queried whether Hipkins and Labour were delaying change to assuage the fears of a noisy minority in the anti-lobby.
Hipkins responded that the Government needed to make sure it was explaining what it was doing around water and why - and to bring people along.
Elsewhere in the interview, Hipkins defended his response to the row over Green Party co-leader Marama Davison's comments over cis white men and violence.
"It's an absolute fact to say that the majority of perpetrators of domestic and family violence are men. Unfortunately, what a lot of men hear when we say that is that the majority of men are committing domestic and family violence. That's not the message. That's not what we're saying at all. But unfortunately for some, that's what they hear."
The Prime Minister said he believed that - as a man - he had a role to call out violence.
"And I think that that's what we're asking all men to do."
Watch Chris Hipkins' full interview above.
Made with support from New Zealand On Air and Te Māngai Pāho.