Secondary school principals are worried by a change that could cut their funding by as much as $6 million per year.
From next year, school operations grants will be recalculated every three months to reflect changes in their rolls.
Education Minister Anne Tolley says the system will be fairer and will encourage schools to retain students.
Budget documents show the change could save the Government $6 million in the first full year.
But the PPTA secondary principals council says it will make planning difficult, especially for schools with transient populations.