The Government reduced funding to more than 330 schools last term because of a controversial new funding system.
Ministry of Education figures, provided under the Official Information Act, show the secondary schools lost a combined total of more than $1.7 million because 4340 students left them between March and June.
The 10 worst-affected schools last term lost between $17,000 and $29,000 each.
Principals say the new system is not reasonable because their costs remain the same even if some students leave during the year.
Freyberg High School in Palmerston North lost $22,000 because of the policy, and its principal, Peter Brooks, says that is unreasonable.
"You don't suddenly not need a classroom because five students have left from that room," he says. "All the costs in that classroom are still the same."
Mr Brooks says his school will be about $60,000 worse off this year because the grants have been adjusted again using September's roll count.
The Government says the money is redirected into programmes providing trade training for teenagers.