Education minister Hekia Parata vetoed a plan to compare charter school students' results with those of children at state schools, official documents reveal.
The Education Ministry proposed the analysis in March this year because it was not going to be done by an independent evaluation of the schools that was published this week.
It said the evaluation by a consultancy firm would not look at student achievement until the middle of 2016, and even then there was no requirement for it to use a "matched group" of students with similar characteristics to the charter school students.
"The ministry intends, however, to carry out such an analysis to supplement the evaluation and is working through the methodological issues involved. For example, the criteria for selecting "twins" will need to be robust for the findings to be valid."
The ministry said similar studies had been done in other countries with charter schools.
But Ms Parata said she did not agree with the ministry's plan.
Her office said today that retrospectively requiring the schools - which the government calls partnership 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."
The documents also show the authorisation board that selects potential charter schools for government approval wanted more focus on the schools' educational achievements in the consultants' evaluation of the schools.
They show the board was not happy with the plan for the consultants' evaluation of the schools and wanted it delayed and re-scoped.
The board had said the evaluation would consider things that were not central to the charter schools' success. The ministry wrote that: "The board does not consider that parent, family and whanau engagement is a critical indicator of the success of the Partnership Schools model."
It said the board also felt the evaluation placed too much emphasis on the extent to which the schools had taken advantage of the flexibility in their funding model.
But the government told the board it was too late to change the parameters of the evaluation, which went ahead and was published earlier this week.
It considered if three of the first five schools set up in 2014 are innovating, but did not compare their results with state schools.
The report found the schools' governance, management and use of funding was innovative, with management split between a chief executive and a principal in charge of education.
Earlier this month, Ms Parata hit back at criticism of charter schools, referring to anti-apartheid protests while criticising secondary teachers for discriminating against staff from charter schools.