"We will be reducing the number of students able to be in the trade academy," Linda Fox, the council's representative on the PPTA board, told the Herald on Sunday.
"It doesn't make me feel very good at all to do that because it's going to lessen the opportunity for those students."
Fox, principal of Kelson Girls' High, said the impact would be felt most in smaller and low decile secondary schools.
She said the funding change would also affect all year 12 students in the schools involved as it would shrink subject choice in academic courses.
"In this latest situation, the ministry has only been able to increase student numbers [in academies] by taking funding from elsewhere in the system," Fox said.
"There are always winners and losers when that happens; the losers are small low-income schools in low-income communities, which need the opportunities offered by a trade academy."
Labour education spokesman Chris Hipkins described the funding change as a short-sighted, cost-saving measure.
"Schools will now effectively be penalised financially when they have pupils involved in trade academies, so participation will inevitably be discouraged," he said.
Claire Douglas, the Ministry of Education's deputy secretary for graduate achievement, vocations and careers, said the funding change was being implemented to correct an anomaly that had resulted in trades academy students being double funded.
The correction would also mean another 300 students could attend trades academies.
Douglas disputed the level of disruption on school staff saying the effect on any individual school would be small, with 80 per cent of schools experiencing little or no change.
However, the ministry's modelling showed 43 schools would lose between one and one and a half days staffing a week.
A further 10 schools would lose between two and four half-days staffing.