The changes were floated by NZQA in 2013 as a way to try to counter the large number of students who entered scholarship exams but never turned up.
NZQA divisional manager Kristine Kilkelly said the fees change would enable the authority to better plan the necessary number of exam booklets, markers, and exam supervisors.
A financial assistance fund was available to help students take part in scholarship exams, she said.
"[Families] that are eligible for assistance, and are paying for one child sitting NCEA, can have their NCEA fee come down to as little as $20. If paying for two or more children, the fee to pay can come down to $30 per family," Ms Kilkelly said. "Students who are granted full financial assistance will continue to be entitled to free scholarship entries."
But Labour education spokesman Chris Hipkins said the new charges could put off students in low-decile schools opting to sit the exams.
"It just creates another hurdle for kids from poorer backgrounds and in lower socio-economic areas.
"It also undermines the monetary value of the scholarships, because some of those scholarships, you've got to do three subjects in them in order to be eligible.
"It is another barrier. And we should be looking to eliminate financial barriers to kids participating in these kind of things."
Secondary Principals' Association chairman Allan Vester, the principal at Pakuranga's Edgewater College, said he did not think $30 was a major barrier, and he was confident top students would be supported by their school if necessary.
"NZQA are correct - lots of students enter and then some/many don't turn up. There might well be a temptation to enter just in case."
Mr Vester said he believed there were bigger issues with scholarship exams - including a big advantage to students who could be put in a special "scholarship class" at school.
"Staffing and time-tabling is much easier in large higher-decile schools, as is staffing the extra scholarship sessions that help the candidates.
"That might well be a factor in the concentration of scholarships in a small number of schools," Mr Vester said.
"Schools might well argue that their success is attributable to the great programmes they run, but I don't think there is any question that economies of scale can assist.
"In schools with smaller numbers ... staffing and timetable constraints make that much harder."
