Te Aupouri is one of four Te Hiku iwi to reach Treaty of Waitangi settlements in recent years.
The Te Hiku Settlement Bill could be passed into law next month, triggering the payment of $21 million in compensation to Te Aupouri, along with farm and conservation land. At the same time, Te Aupouri Maori Trust Board will be dissolved with its assets - and liabilities - absorbed by the new runanga.
Mr Flavell said both he and Treaty Settlements Minister Chris Finlayson were concerned the runanga could be disadvantaged by inheriting a large debt it had not created.
He believed the debt was in the hundreds of thousands of dollars. There was no allegation of fraud at this stage.
"But I will leave that to a good forensic investigation, starting as soon as possible, so this does not get in the road of a successful Te Hiku settlement."
Mr Flavell said he knew of only five occasions in the past when a minister had investigated a Maori trust board, "so it's fairly serious".
In a statement issued late on Wednesday, Mr Subritzky said the trust had closed its Kaitaia offices and halted its social service programmes as of 5pm on Tuesday.
The trust was working with the Ministry of Social Development to ensure other providers took over the trust's community services so whanau did not lose access to support.
Those services are understood to include school-based social work across the Far North, whanau-based social work and children's literacy programmes in Kaitaia, and training unemployed Far North youth to work in the Christchurch rebuild.
Trustee Henry Ihaka of Whangarei did not want to speculate on the cause or the sum of money involved until the board had a clearer understanding of the problem.
"But businesses succeed and businesses fail without any underhandedness, sometimes because people make the wrong decisions. At this stage that's what we think has happened but it's a complex situation."
Mr Flavell's announcement of a ministerial investigation was a relief, Mr Ihaka said.
The board was looking forward to working with an interim manager with the skills and expertise required.
It was providing support for 12-15 staff who were in a "distressing situation".
He hoped they would be hired by the new provider.
"Our people are skilled and passionate in what they do, so we're very disappointed in what's happened," Mr Ihaka said.
The trust board's Project Haere has trained 90 young people to help rebuild Christchurch. More than 90 per cent now have jobs.
The project won the Te Puni Kokiri Award for Excellence in Crown-Maori Relationships just this month.
The other iwi included in the Te Hiku Settlement Bill are Te Rarawa, Ngati Kuri and Ngai Takoto.
Ngati Kahu has not settled.
