Education officials are to change the way charter schools report their NCEA results to bring their methodology in line with state schools.
Charter schools use a different method of calculating their NCEA pass rates to state schools - one which inflates their success.
Education Minister Hekia Parata has been warned by her ministry that an imperfect impression of charter schools' performance is being created as a result.
Advice to Ms Parata shows that when charter schools are measured using the same roll-based methodology as state schools, their pass rates plummet.
The Vanguard Military charter school on Auckland's North Shore reported a 100 percent Level 2 NCEA pass rate, but that fell to 60 percent when the school's results were calculated the same way as state schools report.
Labour's education spokesperson Chris Hipkins said the government had rigged the system to make charter schools look good.
"Clearly the system is being rorted, they want charter school performance to look better, so they're using a different way of measuring it.
"Actually, if they're measured by the same standards as every other school in the country their performance is no better and in some cases significantly worse," Mr Hipkins said.
Mr Hipkins said there was one standard for state schools, another for charter schools.
"Well every other school in the country is measured using a fair method, that includes students dropping out of the system and it means schools aren't incentivised to basically boot kids out to make their statistics look better.
"What's clear is charter schools aren't being held to that same standard."
The ACT Party has driven the charter school model. Its leader, and under-secretary to the Minister of Education, David Seymour, said a different evaluation system was needed for charter schools.
"The reason that there is a difference, just remember, is that we have been pioneering holding schools to account through a contract, and it was necessary if you wanted to do that to have a different system of measurement.
"Now I can understand that has created some confusion, but once you get back to the roll-based evidence, what you discover is that partnership schools are performing pretty well."
Ms Parata is adamant New Zealanders have not being misled about charter schools by the use of two different measures.
But she said she was looking to introduce one standard measure - the one state schools use, in the interests of consistency.
"I want there to be a consistent system, for the purposes of reporting to the government, which is about roll-based, which means everybody who is enrolled at that school counts and how well did they do, versus only those who sat NCEA."
Education officials told a select committee yesterday they were working to fix the way charter schools reported so a transparent and accurate picture of their pass rates could be presented.