Principals say a tougher line on enrolment rules will cause problems for some schools in need of major property work.
They say the Ministry of Education has dropped its relaxed attitude to enrolments, and is basing funding for major building programmes at schools with enrolment zones solely on their in-zone enrolments.
They believe the change is driven by a slew of multi-billion-dollar property issues and will catch out schools with lots of out-of-zone children.
The principal of Paparoa Street School in Christchurch, Philip Harding, said his school needed a lot of building work because of damage caused by the Canterbury earthquakes.
He said the ministry was basing its budget for the work strictly on the number of in-zone students, but figuring out who was in and who was out was not straightforward.
"It's a bit terrifying, because we don't fully trust the ministry to get these numbers right. There are many rules that govern the enrolment scheme legislation, and the status of a parent at enrolment can change.
"So I sense there are going to be many discussions and debates about the enrolment status of various children when we start looking in more detail at our data."
Mr Harding said the regulations have not changed - property funding has always been based on in-zone enrolments at the roughly 800 schools with enrolment schemes.
But he said until now the ministry has not paid a lot of attention to whether schools are sticking to the rules for enrolling out-of-zone students, and some will be caught out by its new, tougher approach.
"The enrolment schemes have been largely ignored and that means that there are some holes where some principals have perhaps exploited the enrolment scheme to their own advantage - that means they've enrolled children out of zone without following all the processes strictly and carefully.
"When they realise that the ministry is getting serious for the first time in many years about managing enrolment schemes properly, I think you'll see a reaction rippling through the sector."
Billions of dollars in property work
Principals Federation president Denise Torrey told Radio New Zealand's Insight the ministry is taking a new interest in enrolment zones because it is facing billions of dollars in property work for problems including leaky buildings and roll growth.
"Our property comes from our in-zone roll and that in the past has been looked at, but not as carefully as it could have been. The more money that's involved here, the more desire I think by the ministry to start looking at how many kids should be at that school and they're not going to pay for property for children that don't belong to that zone."
Ministry of Education head of education infrastructure Kim Shannon said when it started a major property project, it needed to make sure any new classrooms really were needed.
"It wouldn't make sense to build extra classrooms for a school that is experiencing a sudden surge in enrolments from children some distance away, if at the same time there are classrooms sitting empty in those children's neighbourhoods.
"Doing that would lock in major property costs for what could be a short-term fluctuation in a school's roll."
Ms Shannon said schools were free to enrol out-of-zone students if they had the room for them.
She said funding for new or rebuilt property at schools without zones was based on their projected enrolment numbers.