Ending schools' ability to save staffing funding from one year to another will save $58.7 million over two years.
The government is ending the so-called "bank staffing" system in mid-2025 to help cover the cost of teacher pay rises.
Māori-medium schools were exempted from the change.
Principals' Federation president Leanne Otene told RNZ about a third of schools under-used their staffing entitlements each year, a third over-used it and the remainder balanced their staffing.
"It will have an impact. There will be varying degrees of reaction to this.
"But I have a feeling there will be by many schools a little bit of a rethink about how they might plan their staffing each year."
Otene said primary school rolls generally grew as the year went on because more five year olds started school, increasing their staffing entitlement.
Some opted not to use all of that entitlement and carry some over to the start of the following year, but from mid-2025 that would no longer be possible, she said.
Otene said the change would reduce schools' flexibility.
One principal told RNZ his school carried over about $10,000 in staffing funding each year, and found the system very useful.
The change was among savings the government said were needed to help cover the cost of secondary teachers' 14.5 percent pay rise over two years as well as the cost of passing it on to primary and kindergarten teachers.
The Education Ministry said the other savings were over four years and included $40m from the ministry's budget, $219.7m from forecast underspending on teachers, mostly as a result of newer teachers being employed, and $38.9m from deferring building projects at Te Ao Marama and Hobsonville Point Secondary School.