"Despite the extensive work of the commissioner, previous Boards of Trustees, teaching staff and the community, concerns about the College's finances, human resourcing, curriculum and its low student numbers remain," Hipkins said.
"I have considered the submissions received to date and the college's commissioner now has up to 28 days to provide any further information on the proposed cancelation of the school's integration agreement, after which I will make my final decision."
The integration agreement is what the school signs with the Government to allow it to become part of the state system and get funding.
Hato Petera College was first established in 1928 and was one of just five Māori boarding schools in New Zealand.
Its former students include Ranginui Walker, the late emeritus professor of Māori studies at Auckland University; the late artist Ralph Hotere; and prominent Northland doctor Dr Lance O'Sullivan.
Its roll was 210 in 1995, but it has steadily fallen. The final straw was the closure of its boarding school in 2016.
It was left with a single student, Stephanie Pomare, who has lobbied for the school to stay open.