The axe has finally fallen on Hato Petera College, which looks set to close formally after 90 years.

Education Minister Chris Hipkins has announced the cancellation of the college's integration agreement with the state, under which the college was funded, effective today.

Closure is now only a formality to be confirmed by the Catholic Church, which established the college in 1928 on land granted to the church by Governor George Grey for the education of Māori and European children.

For the first 18 years the school was used to train boys as catechists to assist Mill Hill priests in the Māori mission.

It became a general secondary school for Māori boys in 1946 and admitted girls from 1993, claiming to be "the only Māori Catholic co-educational secondary school in the world".

The integration agreement set a maximum roll of 250, but the roll plunged after the Ministry of Education closed the college's hostel for health and safety reasons in 2016 and by early this year there was only one student left, Stephanie Pomare.

Stephanie has now moved to Manurewa High School, saying: "I could have stayed, but there wasn't really much I could do."

Lex Hamill, who was appointed as a commissioner to replace the school board this year, said there were now no students enrolled there.

A group representing two original Māori families who lived in the Northcote area has been occupying Hato Petera College for the past few weeks. Photo / File

Hipkins said the Government and the church agreed to cancel the integration agreement.

"Despite all efforts to find a way of keeping the school going, the reality is that it is no longer able to provide a quality of education," he said.

"Closing schools is never an easy decision. But the roll has fluctuated between one and five this year, down from around 20 last year and just under 50 in 2016, and there are limited opportunities for the students to have social interaction with peers. The classroom environment is lonely despite the best intentions of the staff.

"A further round of consultation has been undertaken by the commissioner since my interim decision at the beginning of June that the school's integration agreement should be cancelled.

"The results of this consultation have confirmed my interim view. The Hato Petera College that exists today is much diminished from the school it was in the past.

"Today's announcement, while sad for those involved, will end a period of uncertainty for students and staff. The Ministry of Education and the Proprietor will provide assistance as needed to help the remaining students enrol at other schools. The Ministry and PPTA will also work with current staff."

Hipkins said the church had told him it would continue to use the site for educational purposes.

"It is now for them to discuss the next steps with the Ministry of Education," he said.

The church initially received 43 submissions from whānau, past students, and staff.

Hipkins said the submissions "tended to focus on the college's history and the pride of former pupils, but not on solutions to the issues the school has been facing in recent times".

The Ministry of Education consulted 18 schools and 17 sector groups.