Concerns also included parent claims of a culture rife with bullying.
Six complaints about the school were made to the ministry last year alone.
A letter sent out to parents and caregivers by the Board of Trustees this afternoon said the Board met with the Ministry of Education and New Zealand School Trustees Association to discuss a way forward.
The letter, signed off by chair Mike Leonard, board member Paula Pusich and principal Raewyn Matthys-Morris, assured parents the school still had a "fully functioning Board".
"Following some lengthy and robust conversation, we have requested MOE support and invited the Ministry to provide that support through a Limited Statutory Manager (LSM).
"We have also requested the support from NZSTA to ensure high-quality governance and leadership of the school."
Four Whenuapai School board of trustees representatives resigned this week and another resigned earlier this year. None of them has been replaced, according to the ministry.
Outgoing board members have refused to comment. It is not known why they resigned.
Parents who have contacted the Herald have spoken of a bullying culture and rapid staff turnover.
A parent, who did not wish to be named, said people coming forward with any complaints were made to feel isolated.
A "mass exodus" of families had been felt in the school community along with a high staff turnover in recent years.
She claimed there were "cases where children were abused on school grounds and the BOT and management refused to acknowledge these legitimate cases ... these families were forced to leave for their safety".
Several parents who have contacted the Herald said they have taken their children out of the school due to bullying, cases of abuse, and dissatisfaction around the handling of these instances by school management.
Education Ministry deputy secretary sector enablement and support Katrina Casey said officials would be working through a range of issues brought to the ministry's attention.
However, Casey said Oranga Tamariki and the police were the appropriate authorities to investigate allegations of any form of abuse against children.
"When we are made aware of an allegation we ensure those agencies have been told and they will then make a judgment on what, if any, investigations or action they will take.
The letter sent out today said an election would be held to fill recent vacancies on the BOT.
Student safety, wellbeing and achievement was the board's "highest priority", it read.
"We can assure you that in line with our Positive Behaviour for Learning (PB4L) school-wide programme and the Vulnerable Children's Act 2014, in any instances of inappropriate student behaviour the appropriate agencies and supports are engaged."
It acknowledged "a number of concerns" raised by the community around leadership and governance and said the board would be collaborating with the MOE and NZSTA around how to strengthen community relationships.
"This will include a review on how we can better manage your concerns and communicate with you going forward."
Summary of Media Council decision
The Media Council has part-upheld a complaint about the New Zealand Herald's reporting on April 25 and April 26 concerning Whenuapai School.
It expressed concern that the articles did not make it clear that no adults were involved in the so-called 'sexual behaviour'.
The first article School in turmoil: claims of 'sexual behaviour' referred to police outlined a number of issues at Whenuapai School including claims of 'sexual behaviour', a bullying culture within the school, staff turnover as well as the resignation of four Whenuapai School board of trustees representatives and a decline in the school roll.
The second article 'Sexual behaviour' claims: Ministry of education asked to intervene at Whenuapai School mentioned a request to the Ministry of Education for support by a Limited Statutory Manager as well as a letter sent out to parents from the Board of Trustees.
The complainant expressed concern that the articles were biased and intentionally misleading; that they expressed only the views of those who were critical of the school; that the reference to "sexual behaviour" put the staff under suspicion and children under stress, when it was on record that the incidents referred to did not involve adults; and that the headlines were click-bait.
The duty editor advised that the school had been approached several times for comment and that other comments critical of the school had not been published.
The term "sexual behaviour" was not used for shock value, but was the term used by the Ministry of Education, which had appointed a statutory manager to take over the running of the school.
The articles did not rely on hearsay. The main points were based on interventions by the Ministry of Education, the police and Oranga Tamariki. The articles also quoted the concerns of some parents who wished to remain anonymous.
The editor noted the article had said 'Both incidents are thought to have involved children' but he acknowledged that a reference to adults not being involved in the incidents, which had been removed in subbing, would have made the situation clearer.
The Media Council upheld the complaint under Principle 1 Accuracy Fairness and Balance, noting that the articles did not clearly state that adults were not involved in the "sexual behaviour".
Also, while noting the Herald had offered the principal and board repeated opportunities to respond to no avail, balance and a fair voice could have been achieved by including the views of those who were supportive of the school.
The Council did not uphold the other aspects of the complaint relating to Children and Young People, Headlines, Comment and Fact and Subterfuge.
The full Media Council ruling can be found at www.mediacouncil.org.nz.
