The previous investigation won the Best Investigative Reporting award at the 2014 World Indigenous Journalism Awards with judges saying it was "an excellent example of the rigour with which we need to conduct ourselves as journalists."
It led to several investigations into the trust and its subsidiary, including one by the Serious Fraud Office. All have previously been reported as finding no illegal activity and no wrongdoing by the trust.
However Native Affairs tonight reported that a review into Te Pataka Ohanga by Internal Affairs had found wrongdoings it described as "gross mismanagement".
These included paying $111000 in directors fees to Kingi Tuiheitia - the Maori King - when he was not a director. That issue had now been referred to Inland Revenue, Native Affairs said.
Te Pataka Ohanga also paid themselves bonuses including koha not approved by the board, and used credit cards to purchase personal items.
It had also allowed board members to take personal loans.
Ousted board member Toni Waho, who spoke exclusively to the programme, said he had one of the loans, which he now agreed was "not a good look".
Native Affairs reported that since then, Te Pataka Ohanga had cancelled credit cards and suspended loans, among other measures to ensure financial accountability.
It was now on an Inland Revenue watch list, and had been given a formal warning.
The show also revealed the trust had made two payments totaling $800,000 for termination fees in 2007.
The trust appointed a new chief executive last month, a former Ministry of Education official named Kararaina Cribb.
Education Minister Hekia Parata appeared on the show, to say she continues to want a change in governance on the board, to a more modern alternative.
Mihingarangi Forbes will now begin a new role with Radio New Zealand.
