A Wellington Girls' College teacher has resigned after allegations he had an inappropriate relationship with a student.

The teacher, has interim name suppression while the Education Council investigates, Fairfax reported.

It was reported the man had a close group of "favourites" at the school.

He described his relationships with students in an email to a former student last year, following the start of the investigation.

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The email, obtained by Fairfax said, "It's very possible that I'm not really cut out for the job that I do. I get results by treating students as peers and expecting the same of a student that I would expect of any adult. Expecting adult relations from students was woefully misguided on my part and probably, ultimately, dangerous and detrimental to the mental health of some."

The ex-student alleged the teacher made sexual jokes to her and other students, Fairfax reported.

He wasn't her teacher, but he created leadership positions that would allow close contact between the pair, it reported.

He also bought her a gift.