National Party education spokesperson Nikki Kaye and Education Minister Chris Hipkins have butted heads, almost continuously, over charter schools since the change of government.

National has lodged a complaint with the Auditor-General over the Government's handling of the potential closure of charter schools.

National Party education spokesperson Nikki Kaye said she sent the letter of complaint on Tuesday outlining what she saw as potential issues to be investigated regarding the Labour-led Government's handling of the potential closure of partnership schools.

The complaint covered two main areas: Education Minister Chris Hipkins' handling of discussions with schools relating to the potential closures, and some ministers' "perceived conflicts of interest".

GRANT MATTHEW/STUFF Hipkins has been clear that a Labour-led Government would always get rid of charter schools. However, the schools that are already open have the option of transitioning to another model, in order to stay open. He says all existing charter schools meet the requirements to become special character schools.

Kaye said Hipkins had made "several unfortunate comments", which indicated he has a "closed mind".

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There was "potential evidence that the schools have undue pressure being put on them to terminate their contracts", she said.

"I believe the minister's and the ministry's process is fundamentally flawed and there is public interest in investigating it."

The future of partnership schools has been under the spotlight recently, with the Government making good on its longtime policy of getting rid of the partnership school model.

Initially it was understood this would mean the existing schools would be forced to close, and no further schools would open under the model.

However, Hipkins has since said the plan was to work with partnership schools to transfer them over to special character schools.

During discussions over the future of the schools, the interests of Labour ministers Willie Jackson, Kelvin Davis and Peeni Henare were called into question by National.

Jackson, Davis and Henare all have connections with charter schools in Auckland and Northland. The group fronted media last week, along with Māori Development Minister Nanaia Mahuta and Customs Minister Meka Whaitiri, to say the plan to "tweak" the designated character model and improve the process of setting up a special character school would accommodate the charter schools with which they were aligned.

The Government introduced its bill to scrap national standards and charter schools earlier this month.

At the time, Hipkins made it clear charter school operators wanting to be involved in education could apply to establish another form of school, such as a designated character school.

It would be up to the Auditor-General to determine if there had been any issues with the process regarding partnership schools and any potential perceived conflicts of interest.

Kaye said she hoped to meet with the Auditor-General in the next couple of weeks.

A spokesperson for Hipkins said neither the minister nor the Ministry of Education had any knowledge of the complaint.

It would not be appropriate to comment further at this point, he said.