The details of the kura's troubles - which started only days into its first term - come as the National-Government sorts through who it will pick for more charter schools next year.
The Ministry of Education and the school say management changes have got the kura, which received an establishment grant of $1.3 million, back on track and student behaviour has improved markedly.
However, partnership school opponents say the early problems at the flagship school - after initial official advice that it needed more time before approval - are serious and embarrassing.
"Why make these kids guinea pigs ... the ones that obviously wanted to learn have been placed in an environment at-risk," said NZ First education spokeswoman Tracey Martin, who has previously raised concerns about the readiness of the kura to open.
The small Northland school sits on a remote farm setting just south of the Bay of Islands with 55 Year 9 to 13 students, some of whom had been out of school for some time.
The public face of the school has been curriculum director Natasha Sadler, who was chosen by the Nga Parirau Matauranga Trust to head the school alongside her relative Glen Sadler.
Documents released to the Weekend Herald under the Official Information Act show the extent of the task became clear almost straight away.
Shortly after opening, Chris Saunders, a facilitator appointed by the Ministry to help oversee the establishment of the kura, forwarded an incident report outlining drug use, bullying, and the use of gang signals.
He again expressed his "doubts and misgivings" about a senior manager - whose name was withheld - after earlier expressing them to a member of the authorisation board tasked with choosing the first schools.
"[Name redacted] is increasingly charting ... [its] own course in a very autocratic matter ... student management issues are already emerging as a threat to the school and there is no coherent plan to deal with behaviour issues."
The following day, the trustees told Mr Sadler and Ms Sadler by letter that they had serious concerns about the kura and Mr Saunders would take immediate overall responsibility for its operation.
In March, Mr Saunders was copied into an "extremely confidential" email from an unnamed person, which reported that "the tension in the kura is high".
"We have managed to 'keep the lid' on this up until now, but unfortunately, the lack of resources (teaching and learning), tensions between co-managers, staffing issues, the us/them divide between teaching and admin staff has finally spilled over."
In releasing the information, Katrina Casey, the Ministry of Education's deputy secretary enablement and support, said the school's issues were resolved or in the process of resolution.
An instrumental change had been the appointment of an interim chief executive, and Mr Saunders would complete his contract this month. Mr Sadler left his role as business director in April.
Some partnership schools were set up to deal with at-risk students, Ms Casey said, and it was "unsurprising" they face "teething issues".
Certain students had been temporarily diverted from the kura into an intensive special education programme, and other initiatives had improved student behaviour markedly.
Since the school opened 17 students have left, and four have joined.
Mr Sadler could not be reached for comment yesterday. Natasha Sadler denied there had been serious issues, and said things had been blown out of proportion.
"Perhaps [media] should be thinking about the fact that we are a brand new school ... we are on the up and up, and things are going really, really well now."
She referred further questions to the trust, who referred them to the Ministry.
