Although the trust had provided a plan for rectifying its issues, she was not confident it would be effective and significant ongoing support from the Ministry of Education would be required.
She said 'partnership schools' were established to cater for children who were struggling and that had to be taken into account. "But it is our duty to ensure they do actually receive the quality of education they need to open the doors of further promise in their lives."
Ms Parata said she was not pre-determining the outcome of that audit. "The issuing of a performance notice is a step in the process to both protect the rights of these students to get a better education while protecting the use of taxpayers' funding."
Earlier this week, Ms Parata was questioned about the school's viability in Parliament and Ministry of Education chief executive Peter Hughes was grilled about it by the education select committee.
The agreement under which the school was established in September 2013 set minimum standards in areas such as achievement and attendance. However, within six months of that, the Education Review Office had warned there were significant problems and the school would need a great deal of support to be effective.
Ms Parata's letter notes that although there were improvements in the management of the school in mid 2014 under an interim chief executive, those had not lasted.
Ms Parata also told the trust that because of the public interest, she would publicly release an Education Review Office review of the school last year which has so far been withheld. She said that review raised concerns about the quality of teaching, the school management, a lack of business expertise, disengaged students and recruitment of suitable staff. She also intended to release the remedial plans the Trust had developed in response, and the Ministry of Educations' advice to her.
The school was one of the first five schools approved under the Government's new 'Partnership Schools' programme. That allowed private organisations to set up and run schools with public funding.
Labour's education spokesman Chris Hipkins said Ms Parata should take responsibility for the plight of Whangaruru charter school because she had allowed it to go ahead in 2014 despite reservations from Ministry of Education advisers.
Mr Hipkins said Ms Parata went against the advice of her own officials by allowing the school to open before it was ready and said she had since tried to cover up the school's problems by refusing to release an Education Review Office report on it.
Ms Parata today said she would release both officials' advice and the ERO report by the end of next week.
Mr Hipkins said the decision by Ms Parata and the Partnership Schools Authorising Board to include Whangaruru in the first batch of approvals was flawed and politically driven. The schools were set up in a rush before they were ready to go and the cost of that was clear almost immediately.
"The Minister was warned the school would not provide a 'safe environment' and its processes were questionable. This is a charter school which has spent its first year plagued by bullying, drug use, absenteeism and management infighting. The ERO has also had ongoing concerns about the quality of teaching, learning and student engagement."
Louise Green, the president of the primary teachers' union NZEI, said students at the school were "caught up in a clash between ideological determination and good advice".
"The breakneck speed at which the first nine schools opened is not helping kids or the well-meaning organisations that are trying to operate them.
"Educators have been greatly concerned from the start about the impact, effectiveness and accountability of these privately-run and publicly funded schools. It's time to put this experiment on ice and instead put the resources into public schools."
The same concerns were shared by Angela Roberts, the head of the PPTA secondary school teachers' union. Ms Roberts said she was not surprised the school was now on notice. "The Minister ignored all the advice and suggested it should open." She was also concerned at the level of support the Ministry of Education had put in to try to make the school work - support she said could have gone on helping vulnerable children in state schools.
"That is because this was all about politics and not about children. So that's a real kick in the guts for the state system."