ACT leader David Seymour says it's too soon to compare charter school results with state schools.
They're an ACT initiative and Mr Seymour, an education under-secretary, is in charge of them.
It's been revealed the Ministry of Education offered in March to compare student results but Education Minister Hekia Parata blocked the survey.
Her spokesman says it wouldn't have been fair to put the schools through it at this time.
Mr Seymour says there will be a rigorous comparison, but not now.
"It's going to take some time to have enough data because the kids have only been there for just over a year," he said on Radio New Zealand.
"There will be an apples to apples comparison ... the only question is exactly how and when."
Labour and NZ First are criticising Ms Parata for blocking the survey.
They say she knows the results will show charter schools are no better than state schools.
There are nine charter schools and the first few opened about a year ago.
They're controversial because they're state funded but can be run by businesses, church or community groups.
They can set their own curriculum and term times and don't have to hire registered teachers.
The rationale for them is that they can tailor their teaching for students who have failed or are under-performing in the state system.
Teacher unions fiercely oppose them.