Police confirmed they had received a complaint from one of the boys' parents but said no crime had been committed and the teacher would not face charges, as the alleged sex was consensual and both students were above the legal age of consent.
The first-time teacher - who the Herald has decided not to name - resigned from the school last week and would not comment when contacted by the Herald yesterday.
"There's certain processes that are in place which are working through things so I'm sorry I actually have no comment about that."
Principal Shane Tong confirmed the woman quit on Friday and yesterday he sent a mandatory report to the New Zealand Teachers Council. He said the school had received two separate complaints from parents of "inappropriate conduct". The school immediately suspended the teacher and began an investigation that resulted in her resignation. Mr Tong would not comment on specific details but said the college, which has a roll of 760 boys in years 9 to 13, was supporting the affected students and had contacted the parents of those who had the most interaction with the teacher. An internal investigation was ongoing.
A spokesman for the Teachers Council confirmed a report had been received and would be referred to the complaints assessment committee.
Hamilton police district child protection co-ordinator Detective Senior Sergeant Nigel Keall confirmed he had received a complaint from one of the students' parents.
Mr Keall would not name the school or the teacher but said the recent complaint alleged sexual contact between a student and teacher.
"We've investigated that and determined that no criminal offence has taken place."
This was because the students were above the age of consent, which is 16, and that the alleged sex was consensual.
He would not say when the complaint was laid.
"Obviously the school are aware of it and the matter is being dealt with."
Mr Keall said police would not take any further action unless new information was received.
The teacher graduated this year and has a three-year provisional practising certificate which expires in July 2017.
Her Instagram account showed photos of herself and a boyfriend with the words "proud teacher #stjohns".
In the 2012-2013 financial year, the Teachers Council referred 39 cases to its Disciplinary Tribunal, a quasi-judicial body that conducts hearings in a manner similar to a court.
Ministry of Education head of sector enablement and support, Katrina Casey, said the ministry was aware a teacher had resigned from the school following allegations of inappropriate behaviour.
Teacher-pupil cases
• In 2013, a male teacher crept into a bedroom where a Year 13 student was sleeping in his house and kissed her. He was later deregistered.
• In 2012, a Wainuiomata High School drama teacher, then 38, resigned when asked to discuss his relationship with a 17-year-old student.
• In 2006, English teacher Natasha Miller, then 23 and teaching at Tararua College in Wairarapa, had an affair with a 16-year-old student. She resigned, and the two gave a tell-all interview to a women's magazine headlined "I fell for my student".
• In 2003, Tauranga schoolteacher Faryn Ripine Matthews admitted sexually violating a former pupil, aged 10. Matthews, 35 at the time, pleaded guilty to three counts of sexual violation and was jailed for four-and-a-half years.
• In 2001, Gemma Aspden lost her job at Broadwood Area School after an alleged affair with a then 17-year-old student.
• In 2000, Janine Rayner confessed publicly to having sex with a Wesley College fifth-form boy when she was a relief teacher there two years earlier.
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