Schools had been threatened with statutory intervention if they did not comply with the law, but some are now seen to be getting away with their protest against the controversial standards with little consequence.
New Zealand Principals' Federation spokesman, Ernie Buutveld, said it was "a serious situation when a quarter of all schools are taking such a bold stance".
He said some schools were facing lower level sanctions, such as not being allowed to join literacy programmes or not becoming host schools for schemes, such as principal mentoring.
But he was not aware of any of the rebelling schools facing any serious consequence.
"The closer we get to an election the harder it is [for the Government] to carry out the threats, I would think, because it's going to look very heavy-handed."
The ministry's programme manager, regional education, Pauline Cleaver, said the ministry was working closely with boards to ensure they met charter requirements.
The action taken against those that didn't would depend on a number of factors.
Some schools were amending their charter to rectify the non-compliance. However, the number of non-compliant schools is higher than it was a month ago.
Ms Tolley said the ministry uses the information in charters to help target resources and support for students and schools which need it most. Those refusing to comply were breaking the law.
"They will miss out on valuable resources to help support students who are failing, while their teachers won't be able to access professional development. These schools will have to answer to parents and their communities."
Mr Buutveld said he was not surprised the number of non-complaint schools was so high as the sector had been trying to get the minister to acknowledge serious flaws with National Standards since 2008.
Labour's education spokeswoman Sue Moroney said the high number of rebelling schools was an indication of a "significant standoff" between the primary school sector and the Government.
"It's a standoff that can't continue if we are going to resolve that issue of underachievement."
Meanwhile, it has emerged that the ministry has accidently approved some non-compliant charters, despite schools deliberately removing all reference to National Standards.
Ms Tolley acknowledged "there were some problems in the ministry".
"My understanding is that the ministry has now contacted all of those schools and informed them that they were not compliant, and it is working with them to ensure that they are."