UPDATED 4.49pm Marlborough Girls' College is undertaking a review after a transgender student began a petition over which bathrooms she could use.
LISTEN ABOVE: Marlborough College acting principal Jo Chamberlain talks to Larry Williams
Stefani Muollo-Gray says she's been told to either use the boys or unisex bathrooms after a teacher at the school questioned which toilet she used.
She's started a petition which now has over 5000 signatures.
But, acting principal Jo Chamberlain said when first enrolled, the 16-year-old and her parents agreed she would use the boys' bathrooms.
"We've met with the student and immediately agreed to undertake a review. The college is really committed to getting this right for this student, but we're very conscious of getting it right for the rest of our student body too."
Stefani Muollo-Gray denies agreeing to anything when she began.
Ms Chamberlain said she really wants to protect the student.
"And that's where we become really vulnerable in schools, because she is a real priority, but it's really important when public information goes out we have the opportunity to present the facts as we see them."
Minister of Education Hekia Parata said she knows the school is working hard to resolve the issues, indicating an agreement had been previously reached on which bathrooms Ms Muollo-Gray would use.
"There are other girls at the school who have different views and the school has to balance all of those. I think that they have managed incredibly well to this point."
Family First National Director Bob McCroskie said the legal opinion sides with the school.
"School toilets, showers and bunk rooms at camps and sports teams should be based on biology. Biology is an objective reality as opposed to just a subject of assessment of how someone feels."
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