Schools that refuse to comply with national standards requirements could face funding cuts, Education Minister Anne Tolley says.
The standards regime has come under fire from teachers, parents and academics, concerned at the speed of its implementation and the effects it would have on children who were falling behind.
Education Ministry figures show that, as of yesterday, more than a fifth of schools have submitted their annual charters without the required national standards targets.
Of the 1922 charters from English-medium primary schools analysed, 1503 complied with the requirement.
"Some schools have shown that they are having difficulty about how they set the targets, so we've had someone working with them, helping them develop that and we're just working through that process," Ms Tolley said.
However, a number of schools that have deliberately chosen not to include the targets in protest of national standards.
"They're breaking the law," Ms Tolley said.
"That information will then be used to provide extra help around students, provide targeted professional development for teachers...so if they've have chosen to break the law and don't have the data they won't be able to access that targeted assistance."
Ms Tolley said the ministry was still in touch with the schools attempting to boycott the standards, encouraging them to submit legal charters.
Labour MP Kelvin Davis said the continued defiance from schools said a lot about national standards.
"Parents around the country continue to stand up for their children in the face of threats and intimidation, including the possibility of having Boards of Trustees of high performing schools being overseen by a statutory manager or even being replaced by a commissioner," Mr Davis said.
"It will be interesting to see what tactics the minister pulls out of her hat to force boards of trustees to comply."