The existing school will continue operating until the new kura is complete.
The new building will accommodate up to 150 students and can be expanded to cater for up to 200.
Ministry's head of education infrastructure service, Kim Shannon, said staff and the principal of Whirinaki School were expected to run the new kura.
"Staffing numbers in schools and kura are dependent on the student roll, which can fluctuate from one year to the next. There can also be changes in staffing due to promotion, resignation or retirement," she said.
In 2014, a row erupted between the ministry and the local community which wanted the existing school at Whirinaki expanded instead of being moved to a new site.
The dispute reached the Environment Court and a special three-day hearing was held at the Copthorne Hotel at Omapere.
Te Kura Kaupapa Maori o Te Tonga o Hokianga was granted wharekura (high school) status in April 2010, entitling it to extra accommodation and classrooms.
The ministry opted for relocation rather than expanding the existing school because of the risk of flooding, land availability and tenure.
Hokianga resident Diana Ellis of Te Hikutu hapu, who represented herself, and 11 witnesses at the court hearing, yesterday said she opposed the new site for environmental reasons.
She said the quality of the harbour water and the kaimoana in it were crucial to the wellbeing of children.
"I am a strong advocate for the development of the new Kura Kaupapa, indeed any development that benefits the people of Hokianga.
"But I vigorously oppose to the location for the new kurakaupapa at Koutu Point for environmental reasons.
"The main concerns are the environmental impacts on the Hokianga harbour from outfall of stormwater and the onsite sewage treatment system."
But the ministry argued any adverse environmental effects from the proposal would be less than minor, and could be mitigated with conditions imposed.
