Gary Bramley of Kaeo, spokesman for the whanau who withdrew their children, thanked the Ministry for listening to their concerns and carrying out a thorough investigation.
The ousted board has said the dispute centres on the dismissal last year of previous principal Louisa Mutu and the efforts by a group of disaffected parents to have her reinstated.
Dr Bramley, however, said the real reasons for the exodus were parents' "real and escalating concerns" about pupils' physical safety; bullying of staff by board members, including a lock-out and threatening emails sent on Christmas Eve; the lack of a formal election process; and a lack of transparency and accountability.
He said parents took those concerns to the board at the end of 2013 but members failed to act or engage. When the parent body of kura kaupapa in New Zealand, Te Runanga Nui, also stopped engaging, parents felt they had no choice but to remove their children.
"Our view as kura whanau is that any publicly funded school that manages to lose half its qualified and capable staff and more than half of its students in a matter of weeks deserves a high level of public scrutiny," Dr Bramley said.
The issue has sharply divided the Whangaroa community. The chair of Te Runanga o Whangaroa, Arena Heta, has welcomed Mr Forbes' appointment, saying the arrival of a commissioner was no surprise to locals.
"The only surprise is it has taken so long when we first wrote to Minister Parata in January," he said.
Others support the ousted board with former chair Terry Smith and current parents penning an open letter denouncing the Ministry's "heavy-handed" intervention.
The appointment of a commissioner should have been a last resort but was instead an example of the Ministry's "paternalistic arrogance of telling us they know what is best for us".
They said the principal and former board had full support of whanau, and the children were settled, happy and engaged.