The Post Primary Teachers Association (PPTA) is worried the government will cut funding for small secondary schools as part of its school funding review.
The PPTA said the review appeared to be targeting the base staffing that ensured small secondary schools had enough teachers to offer a range of subject choices.
The review has not proposed a cut, but said there were opportunities to reduce base resourcing for schools and provide more on a per-student basis.
It said primary schools would probably struggle if their base staff was reduced, but staffing allocations for small secondary schools were generous.
"The level of base staffing provided through these arrangements appears relatively generous compared to primary schools. And unlike primary and intermediate schools, base staffing entitlement is not withdrawn or abated as roll size increases beyond 200 students.
"These elements are key drivers of the high average per-student cost of small year 9 to 13 secondary schools," the document said.
That's worried the PPTA and the union's Taranaki regional chairperson, Erin McDonald, said reducing base staffing for small secondary schools was a bad idea.
"In a small secondary school, in order to offer a range of different subject choices there needs to be a range of specialist teachers, and by removing that mechanism within the funding it means that schools are going to be put under pressure to reduce the number of courses that are available to the students."
Ms McDonald said small schools already did some teaching via the internet, but that would not work for a lot of subjects.
"You'd struggle to deliver a Level 3 chemistry course online because you've got students who need to carry out practical experiments using chemicals and specific equipment."
Secondary Principals Association president Sandy Pasley said it would not want to see any big changes to base resourcing for secondary schools.
Their staffing needs were quite different to primary and intermediate schools because they had to offer a range of subject options, she said.
"When you're getting into the senior secondary area, in terms of [years] 11, 12 and 13, you need to be able to offer students a reasonable choice and if it's all per-student funding that could be under threat for small secondary schools."
Education Minister Hekia Parata said small schools were an important part of the education system.
"I have every intention of ensuring that we support small schools to be educationally viable. This is because small schools are an important feature of our education system and an option that many parents choose for their children."
The review document said there were very few small secondary schools.
"Among secondary schools 7 percent have a roll of 200 or less, while 2 percent have a roll of 100 or less," it said.
Small primary schools were much more common.
"In 2015, 33 percent of contributing and full primary schools had rolls of 100 or fewer students, and 19 percent had 50 or fewer students."
The document said base curriculum staffing for secondary schools provided the equivalent of about 1900 full-time teachers.