Government research shows most of the low-income families receiving a state scholarship for private schools are being left out of pocket, often by thousands of dollars.
Families receiving the $16,500 a year Aspire scholarships have told the Ministry of Education the money does not cover all the costs of private schooling.
The Education Ministry surveyed 85 caregivers whose children got the first round of Aspire scholarships starting in 2010.
Of those, 70 say the scholarships do not cover all school fees or course-related costs.
They say the extras - which can include additional school fees, uniforms and transport - can add up to thousands of dollars.
Auckland's Kristin School executive principal Peter Clague says some schools waive those extras for scholarship students.
"Our approach has been to bear the burden of those extra costs inside the school so that we can genuinely make it as easy as possible for people to be educated here."
Mr Clague says schools should ensure families know what they are in for financially when a student takes up a scholarship.