Charter or partnership schools are privately run but publicly funded and were introduced in New Zealand as part of Act's confidence and supply agreement with National.
Recently released Ministry of Education documents show that Ms Isaac had expressed the authorisation board's concern with the evaluation plan.
The Ministry wrote to Ms Parata on March 17 to say it did not agree that a comparison between the achievement of students in partnership schools with a matched group of students in state schools needed to be included.
Such a comparison was not practical because charter or partnership schools had only been operating since 2014.
"The Ministry intends, however, to carry out such an analysis to supplement the evaluation, is working through the methodological issues involved, and will consult with the board on this work," the document stated.
Ms Parata drew a line through that statement and wrote: "do not agree".
Labour's education spokesman Chris Hipkins said that intervention was bizarre and showed Ms Parata was scared of what a proper evaluation would reveal.
"Why would she not want them to carry out that evaluation if the Government was confident that charter schools are going to deliver better results that state schools, why would they be afraid of that sort of analysis?
"It seems to me that Hekia Parata didn't want the analysis done because it almost certainly would show up that charter schools aren't performing in the way that the Government promised that they should be."
Ms Parata's office has been contacted for comment.
Mr Seymour, Under-Secretary to the Minister of Education, said that, despite his initial request for MartinJenkins to re-scope its first evaluation, he was now happy with a decision for more quantitative comparison of partnership students with comparable students in state schools to be carried out in future reviews by the consultancy firm.
"I believe and I think the Minister believes that we want to do a quantitative comparison that answers the question - looking back several years as it is too early to say now - has the partnership school model led to gains for kids that they might not have made without the model?
"We have said, look, we can't achieve everything out of the MartinJenkins report straight off...but we will use data that the Ministry has to achieve that in time. But you can't do it in the first report."
A spokesman for Ms Parata said that "retrospectively requiring the schools to jump over another hurdle shortly after they had been established was not in the best interests of students".
"Partnership schools are already contractually required to demonstrate they are lifting student achievement and meeting Government targets.
"There is a wealth of information publicly available about their performance for people to make their own comparisons. In addition they are subject to review by the Education Review Office."
