Curriculum director Natasha Sadler — the driving force behind the school and the author of its curriculum policy — will lose her position and the role of its general manager, Makere Laurence-Bade, will be dissolved.
Ms Sadler has been offered a fixed-term contract as a teacher. She will have extra duties while a new principal is recruited.
The trust was also in line for a shake-up and was working to attract new members, Mr Johnstone said.
"We have had lots of offers of help, which is encouraging. We are getting some help from Te Puni Kokiri and have approached Maori academics for their advice." A recruitment process for a new principal would begin as soon as possible.
The school has been open for less than 18 months, at a cost of $3 million to the taxpayer. It teaches five core subjects and a handful of optional subjects to 34 students aged between 13 and 18.
Even before opening, the school was plagued with problems including staff infighting and local opposition after a lack of community consultation. In its early days the school struggled with student drug-taking, gang insignia, bullying, teaching quality, recruitment and governance.
Ministry documents, including the advice which sparked the minister's 28-day warning, laid the blame with the board of trustees.
"The [trust] continues to demonstrate a lack of necessary educational expertise to ensure effective leadership of the academic aspects of the school," the report read.
It also referred to Ms Sadler saying: "This project may be at risk because so much depends on one person."
Both Mr Johnstone and Ms Sadler said they felt the leadership difficulties could have been avoided if the ministry had been more straightforward in its demands.
"Up here in the north, people[tend to] speak their minds. So when you're not told directly what to do, it can be difficult," Mr Johnstone said.
Ms Sadler said she knew there had been criticism but she had undertaken training from an external provider brought in by the trust and felt she was improving. "I'll be honest with you, it has been said there was a single-eyed, my way or the highway approach, but that has changed."
She was disappointed in the trust. "If someone had just said something earlier, there may have been a different discussion to be had right now. I'm disappointed people didn't talk to me. I'm doing the best I can."