School staff are required to be vaccinated within two weeks, but a lack of information and unclear guidance has Otago and Southland principals navigating a "minefield of interpretations".
Recently the Ministry of Health announced school staff and support people must have their first dose by November 15 and be fully vaccinated by January 1 next year to have contact with children and pupils.
The mandate includes all support people in schools and early learning services, such as teacher aides, administration and maintenance staff and contractors.
Earlier this week Secondary Principals Association president Vaughan Couillault told RNZ there could be thousands of teachers resisting getting the vaccine.
Southland Primary Principals Association president Simon Bell said he knew of some schools in Southland which would have at least one teacher holding out.
Schools with staff who did not have the vaccine by November 15 would be in a difficult position, as there was a shortage of reliever teachers at the moment.
The depth of the issue would vary from school to school, but there were unclear aspects of the mandate which would affect every school.
One of those issues was whether parents would need to be vaccinated if stepping on to school grounds, he said.
"It’s a real minefield of interpretations."
Otago Primary Principals’ Association president Gareth Swete said the issue was challenging to navigate.
The information released by the Ministry of Health had a lot of "grey areas" and more clarification was required.
Those grey areas had rightly caused a lot of anxiety among some teachers in the region, such as what classified as an acceptable vaccine exemption, he said.
It would take time before the system was running smoothly, he said.
Otago Secondary Principals’ Association president Lindy Cavanagh-Monaghan said there was a tension between the personal views of some teachers and what the Government had mandated.
A range of possibilities were being considered for teachers who refused to get the vaccine, such as a suitable exemption, teaching in personal protective equipment gear or alternative work off-site, she said.