The principal of a new charter school has resigned, less than two weeks after the institution opened, while he is investigated by the Teachers Council over exam entries.

A former deputy principal of Auckland Grammar has replaced him.

James Haggett resigned as principal of Middle School West Auckland on February 3 - the students' first day - after it surfaced he was dealing with an investigation by the Teachers Council regarding the administration of examination entries from 2013.

A mandatory report was laid in December by Haggett's former employer, the Catholic Auckland boys' school St Peter's College, where he had been deputy principal in charge of curriculum. The Weekend Herald understands Mr Haggett left St Peter's in August.

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Mr Haggett could not be contacted for comment. But in a statement a week ago he said: "While at St Peter's College I made an administrative error and compounded that by continuing with the process as opposed to correcting it immediately. It involved nothing financial."

Schools are compelled to report to the council if there is reason to believe there has been serious misconduct, if there are issues with a teacher's competence or if a teacher resigns in adverse circumstances.

Usually, teachers are stood down until investigations are complete, but charter schools are not bound by the same rules as state entities.

The academic manager of the Villa Education Trust, which owns Middle School West Auckland, Alwyn Poole, confirmed Mr Haggett's resignation yesterday. He said the decision to resign was entirely Mr Haggett's.

"James wanted to give himself every ability to put the circumstances of the complaint behind him," Mr Poole said. The school had already made a new appointment.

"We completely did not want to go through a situation like that in the first week of the school but ... when working with kids you have to quickly move on."

The new principal was Alex Metzger, who was deputy headmaster at Auckland Grammar for 20 years.

Mr Poole said Mr Metzger had already been spending time with students and would start on Monday, February 23.

"We are delighted with Alex. I think he will be an outstanding principal and the children, families and staff at [the school] will be very well cared for under his leadership."

Middle School West Auckland is the second charter school to open under the Villa Education Trust umbrella. The school is a co-educational middle school - Year 7 to 10 - in West Auckland.

Charter schools, which get government funding, have been controversial in that they can teach any curriculum and teachers do not have to be registered. They are also not subject to the Official Information Act.

Post-Primary Teachers Association president Angela Roberts said she felt the whole incident was an example of a system with very little transparency.

"There is a complete lack of accountability. There are no standards or rules around this, whereas if teachers are in the public system there would have been a clear process from the start," she said.

Education Minister Hekia Parata was unaware of the resignation yesterday. She said unlike in state schools, the sponsor, not the ministry, was the principal's employer.