A group of 89 secondary school principals are calling for an immediate halt to plans to replace the NCEA school qualification.

In an open letter to Education Minister Erica Stanford and Acting Secretary for Education Ellen MacGregor-Reid, the group said the plan lacked a clear rationale and posed huge risks for disadvantaged students, including Māori and Pacific teenagers.

"The proposed system is designed for university-bound students at the expense of students with other strengths and pathways," it said.

The proposed change announced earlier this month would replace Levels 2 and 3 of the NCEA with a certificate and advanced certificate of education, while Level 1 would be dropped for a foundation certificate in literacy and numeracy.

It would also prevent schools from mixing standards from different standards and require students to pass four out of five subjects each year with achievement marked with letter grades and an overall score out of 100.

The principals' letter said the proposal was premature because the senior curriculum the new qualification would assess had not been completed.

It said the decision was made with limited sector input and lack of transparency.

"Principals involved in consultation have been subjected to restrictive non-disclosure agreements," the letter said, referring to a group of 14 principals that initially advised the government on the proposal.

The letter said there was "strong opposition" to introducing rigid subject boundaries and removing the Level 1 certificate risked leaving some students with no meaningful formal qualification.

"The proposed system is likely to disadvantage many students: Māori, Pasifika, neuro-diverse, migrants and second language learners, transient students and those from lower socio-economic backgrounds," it said.

The letter urged the government to improve rather than replace the existing NCEA.

"Replacing NCEA is politically driven rather than educationally necessary," it said.

"The shift to letter grades and percentages is a regression to outdated, hierarchical models that will likely lead to scaling, bell curves and league tables."

Papakura High School principal Simon Craggs said many, but not all, of the signatories were from schools in communities facing high socio-economic barriers.

He said aspects of the proposed change were similar to old-fashioned qualifications like School Certificate, which allowed only 50 percent of students to pass.

"A lot of us remember what it was like for kids in lower socio-economic areas under School Certificate, and we feel that a lot of the elements of this new proposal are a return to that type of assessment," he said.

"There needs to be a much greater conversation that happens before such a drastic measure could be should be even be considered. We don't feel that enough principal and educator voices have been heard."

Craggs said it was not true that NCEA did not work well for academic students and subjects.

"There's a a bit of a manufactured crisis around NCEA not meeting the needs of academic kids," he said.

The Education Ministry and the Education Minister were asked for comment.