The school, on a farm 65km northwest of Whangarei, was one of five chosen after a lengthy selection process to prove privately-run, publicly-funded schools can work in New Zealand.
When problems including management infighting and serious health and safety issues such as bullying and drug use were revealed in June, the ministry said the school's issues were resolved or being resolved.
But ongoing problems at the school include the quality of teaching, learning, management, leadership and student engagement.
The school's roll was 47 last month - well below its guaranteed minimum roll of 71 and the 61 students who started the year.
Reports on all charter schools were recently published - except for the "readiness review" of Whangaruru.
The ministry's head of sector enablement and support, Katrina Casey, said the school's report was received from the Education Review Office near the end of September.
It found issues with the quality of teaching, learning, management, leadership and student engagement.
"While progress has been made in these areas, there is still work to be done ... we will continue to monitor the performance of the school against its contract to ensure that what is set down in the contract is being done.
"We will also closely monitor the school's resolution of the issues raised in the ERO readiness report, which we expect to happen in a very timely manner."
Ms Parata said partnership schools were working with students who had been out of education for a long time and "the fact they're now back in education is significant".
Whangaruru had some particular challenges in the first year and had been given time to address these.
"There are contractual provisions that bind the school and the ministry and they're acting in accordance with those provisions. Whangaruru knows it needs to do better."
Labour's education spokesman, Chris Hipkins, said there was clear evidence the school was not ready to open before the first school day, and Ms Parata had kept her "head in the sand" ever since.
"This is a failed model. It was supposed to be about giving kids a better chance, and this school is clearly failing and the Government isn't doing anything about it."
The school, which is run by the Nga Parirau Matauranga Trust, did not respond to a request for comment.
Trustees have previously blamed the drop in enrolment on the school's isolated location and media scrutiny.
Charter schools
What are charter schools?
Charter schools, officially called partnership schools in New Zealand, are publicly-funded but privately-run. More common in the United States, the model was first established here this year, with five schools opening.
Why were they introduced?
They were established under a confidence and supply agreement between National and the Act Party following the 2011 general election. They offer choice to parents whose children were being failed by the standard school system, the Government says, and innovations could be adopted in the state sector.
How have they performed so far?
End-of-year results are not yet known, however according to a June Cabinet paper four of the schools have shown strong progress, while Te Kura Hourua ki Whangaruru faces continuing issues. An independent evaluation of the partnership school model will be staged over four years, with the first report due early next year.
How many more will be set-up?
Four more charter schools will open next year, bringing the total to nine. There is no indication yet on whether more will open in following years.
