Treaty Negotiations Minister Andrew Little received nearly 50 formal complaints by seven iwi before he signed the Pare Hauraki settlement last year.
Six of the iwi will oppose the settlement again today at the start of a week-long urgent Waitangi Tribunal hearing in Wellington.
Claimants are set to receive $100 million through the collective settlement, after Crown actions left them virtually landless.
But many neighbouring iwi argue the settlement also includes rights and land situated within their own tribal boundaries.
Several attempts by Tauranga iwi Ngāi Te Rangi to resolve their overlapping interests have failed. In May last year they brought the wrath of their people to the steps of parliament.
Figures obtained by RNZ show the treaty negotiations minister Andrew Little received 47 formal complaints by seven different iwi before he signed the Pare Hauraki deed of settlement in August.
Mr Little said he did not regret his decision.
"The Hauraki issue is a very complex issue. There are a large number of iwi, both Hauraki and non-Hauraki iwi who have a stake in what is happening.
"I've got to balance the interests of all of them and I'm satisfied with where things are at."
Ngāi Te Rangi have maintained they hold mana whenua (absolute guardianship) over the Tauranga Harbour.
Ngāi Te Rangi chairman Charlie Tawhiao said the process was gruelling and his iwi was up against two formidable opponents - the Crown and Hauraki lawyer Paul Majurey.
"Neither of whom can be underestimated, [they're] very, very capable leaders in their own right. So it's been gruelling and also hard not to be aware of the responsibility of getting it right, that's pretty scary," Mr Tawhiao said.
"But one of the things that's sustained us, and you'll see it in the people here, is the feeling and the sense that right will prevail."
Iwi chief executive Paora Stanley said the Waitangi Tribunal hearing would give the iwi a chance to explain why the Pare Hauraki settlement threatened that status.
"There's a lot at stake in terms of our mana whenua status and I think we're walking into this with open hearts and open minds."
Ngāti Wai, an iwi based from Tapeka Point in the Bay of Islands to Matakana in Mahurangi, will also stand before the tribunal.
Ngāti Wai spokesperson Aperahama Edwards said the Crown had wrongly granted Hauraki tribes governing and purchasing rights.
"We see this as an opportunity to be able to voice our view and our opinion in terms of what is absolutely unjust and not pono [honest] or tika [true]."
He said the Crown had largely ignored the iwi's overlapping claims and failed to engage with them at every step of the process.
"We have tikanga that we could fall back upon to help guide and facilitate central discussions that really should have happened right from the outset. This whole thing has been done in the dark.
"Instead of being a process to work through historic grievances, all it has done is create new ones."
But Mr Little is confident he did everything in his power to resolve overlapping issues among iwi.
He removed governing rights over the Tauranga Harbour from the settlement and said he encouraged iwi to find a solution through a tikanga-based process.
"Nothing was moving and if I had to level criticism I would be levelling it at a number of different quarters. In the end something had to happen to get things moving. It is now moving.
"Iwi who are concerned are exercising their legitimate rights to test their view before the tribunal. That is now happening and I await the outcome of that process."
The Waitangi Tribunal will hear from Ngāi Te Rangi, Ngāti Porou ki Hauraki, Ngātiwai, Ngāti Manuhiri, Ngāti Ranginui and Waikato-Tainui.
Each of them alleges the Crown breached the principles of the Treaty of Waitangi through its overlapping claims policies regarding the Pare Hauraki Settlement.