Maniapoto challenged his argument: "Everybody, all the experts - the Heather Simpson report, the Māori health advisory group, all the NGOs that wrote to you and David Seymour last week, the Waitangi Tribunal with its interim recommendation - they all say that we need an independent Māori authority that will work in a certain way. Why do you not trust expert advice?"
"Because I think it will end up creating a massive amount of bureaucracy," Luxon said.
Maniapoto alleged he was peddling "misinformation" about competing health systems.
Both Luxon and Act's David Seymour have promised to scrap the Authority if elected in 2023.
On the questions of Māori co-governance and Te Tiriti, Luxon said he was open to discussion, but that he and National firmly opposed two-system governance.
Maniapoto suggested that throwing allegations of "separatism" into the mix was not helping the conversation. Luxon denied that: "I'm not. I'm saying two systems don't work for us, right?"
Quizzed over his knowledge of Te Tiriti and whether he believed that Māori at the time of signing would really have ceded their sovereignty to the Crown, he referenced Article 1 of the English version rather than the Māori version.
The English version states that Māori gave the Crown "absolutely and without reservation all the rights and powers of sovereignty over their lands".
Te Tiriti reaffirmed Māori sovereignty and agreed to share authority with the Governor to ensure Māori interests were protected.
Luxon said the Government needed to be upfront with the New Zealand public about how it was interpreting the Treaty.
When asked about going into next year's election, Luxon acknowledged there's definitely more room for Māori candidates in National's caucus, saying that the party doesn't have enough of "a Māori voice within it".
But he's confident that the party will go into next year's election with some "outstanding Māori candidates", based on outreach conversations he's had over the summer.
"I'm thinking of two or three [candidates] already that we've had conversations with," he said. In terms of his own journey with Te Ao Māori, Luxon admitted that he had "very little exposure" growing up in Christchurch.
He also admitted last year that his role as National's iwi development spokesman was "difficult" as a non-Māori, because he didn't have the right "lived experience".
But now he's actively working to improve his understanding of Te Ao Māori he says, and he's booked in to start te reo lessons once a week.
• Te Ao with Moana airs on Māori Television, Monday nights at 8pm