Teachers were locked out for two weeks in January, and a number of staff resigned or took sick leave. At the start of the school year parents pulled about 50 children from the kura.
Most have gone to neighbouring Matauri Bay School, which has had to provide extra classrooms and hire staff to cope with the influx, while the older students have gone to Whangaroa College, in Kaeo.
The school had previously been run by a group of parents, who say the kura kaupapa governing body Te Runanga Nui led them to believe their informal board was legal.
Many were caught by surprise by last year's board election, and questioned whether proper processes were followed.
Parents initially approached Education Minister Hekia Parata and ministry officials since January, with little result, but the ministry has now asked the board for evidence that it was legally elected. It is understood the deadline passed on Friday.
Katrina Casey, head of sector enablement and support, said the ministry was investigating whether the elections met the appropriate criteria, following a complaint.
"If we find that they didn't, then we would appoint a commissioner whose responsibility would be to run a new election process as quickly as possible for the kura," she said.
She was expecting a decision within days.
The ministry earlier said it was aware of the drop in the kura's roll, saying it would be concerned if it affected student learning. It would not comment on the reasons for the exodus, but said the board had kept officials informed of issues facing the school and community.
It is understood that Miss Mutu has lodged a claim of wrongful dismissal.