The board was subject to a review by Ernst and Young and Charities Service while its subsidiary Te Pataka Ohanga was looked at by the Serious Fraud Office.
The reports cleared them of criminal or unlawful conduct.
But Ms Parata said they found "a number of unacceptable practices, made very serious observations and provided recommendations that require remedial and sustained steps to be in place."
The Trust Board has informed Ms Parata that after consultations throughout the country, some regions wanted the board to stay the same and they wanted the same board that lodged the Waitangi Tribunal claim to negotiate with the Crown.
Before she went public last week, Ms Parata wrote to the board asking that it honour the understanding they had reached last year that a modern model of governance be put in place.
She acknowledged that the board had changed its deed so that trustees were no longer members for life but said that was not enough.
"I expect to see a process and model of governance that reflects the principles of representativeness, transparency, accountability, and auditability."
But the board was in control of the whole process.
In her letter to kohanga reo, Ms Parata said "when an open process has put a new structure in place it will be up to any new board to decide who represents you in discussion on [the Waitangi Tribunal claim]. If a new board chooses current trustees to represent you, then I will be happy to work with them."
Trust board co-chairs Timoti Karetu and Tina Olsen-Ratana wrote to the kohanga reo: "It is unfortunate that there is a clash of this kind and disappointing that the minister continues to ignore the mandate you have given to us as your board....
"We must remain steadfast in our focus for resolution that is appropriate. Remaining united in our pursuit for equity and recognition of this precious taonga, kohanga reo kaupapa, is imperative."
Both the National Trust and the Ministry of Education have published the letters on their websites.
