Education Minister Hekia Parata says she does not accept figures showing that five new charter schools are receiving significantly more funding, per student, than schools in the public sector.
Labour says one school in particular will receive more than $40,000 for each of its 50 students, compared with an average of about $7000 per child in state schools.
It says the funding for the other four charter schools ranges from $9688 per student, to $21,247.
Education spokesperson Chris Hipkins said it points to an unfair bias towards charter schools.
Ms Parata said public school funding could be manipulated to come up with similar figures.
But she acknowledged smaller schools do cost more to run, which could be reflected in the per student funding.
The Secondary Principals Association says the Government needs to explain the high per-student funding rates.
It says charter schools might deserve higher rates of funding if they are working with difficult students who do not cope in mainstream schools.
But it wants to some justification for the figures.