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Parents of school pupils were told in an update sent on Thursday that Logan Park High School co-principal Kristan Mouat had not been vaccinated and would begin the school year working remotely.
Assistant principal John Major said in the update Ms Mouat was not vaccinated "due to medical reasons".
Ms Mouat would not have physical contact with pupils, he said.
Mr Major said the school was fully compliant with the vaccine mandate.
Pupils would still be able to make online appointments to meet Ms Mouat and she would still be able to have face-to-face contact with parents and staff.
"She will continue all the usual strategic, curriculum and leadership work."
The school would continue to work with the board of trustees to ensure compliance with the mandate and there would be no additional costs to the school with the working arrangement, he said.
Pupils return to the school on Wednesday.
Ms Mouat declined to answer questions about whether she had a medical exemption to not receive a vaccination or if the quality of education provided at the school would suffer as a result of her working remotely.
She referred questions to board of trustees chairman John Bradfield, who said he had nothing to add to the message sent out to parents by Mr Major.
In November, the Ministry of Education detailed the process for school staff who needed an exemption. It said only those physically unable to tolerate the Pfizer vaccine would get an exemption, which would be about 100 to 200 nationally.
If a staff member was issued an exemption, it was recommended the board carry out a health and risk assessment in consultation with the employee to determine what measures could be put in place to minimise risks to the exempt person, other staff and pupils.
Ministry of Education leader south Nancy Bell said the board of trustees employed school staff and was responsible for ensuring the school complied with the mandate. The ministry did not hold vaccine status information.
Boards made decisions on how to manage employees who had not met vaccination requirements.