Principals estimate several thousand school staff are resisting the government's directive to get at least their first Covid-19 vaccination before 15 November.
They say some are presenting apparently bogus exemption certificates which are causing confusion and they are waiting on official guidance so they can bin them.
School and early childhood staff who have contact with children must get their first vaccination by the middle of November and be fully vaccinated by the start of January.
There is no official tally of how many teachers and other school staff are vaccinated and how many have not even had their first injection.
Secondary Principals Association president Vaughan Couillault said anecdotally it appeared most secondary schools had a handful of hold-outs which suggested there could be a couple of thousand across that sector.
"We're hoping that that handful of five goes down to one at the most but even then that's still 400 - 500 teachers across the network you're going to lose which will be very difficult to find," he said.
Couillault said schools had plenty of support and information to help persuade vaccine-hesitant staff to get the injections but schools would not know if they had been successful until the deadline.
"People's views of what they're going to do may change when it becomes a reality that actually at the moment, as written, the 15th is a hard deadline and people at the 11th hour might change their mind because on the 16th it could, it could impact their employment," he said.
On that date, they would not be allowed in schools unless they had received at least their first vaccination and the Education Ministry has advised schools that unvaccinated staff could then be placed on leave without pay.
Couillault said some of the staff refusing to be vaccinated said the vaccine mandate was not right and others were worried about pre-existing medical conditions.
Principals Federation president Perry Rush said most primary schools had at least one staff member resisting vaccination, a figure that, as in secondary schools, would equate to a couple of thousand people.
"We certainly are hearing questions arising from some schools and I think most schools have a need to address a staff member or several staff members who might be in a position of questioning this for themselves. So it's an issue, we don't hear that it's a significant issue, but an issue nonetheless."
Rush said establishing if staff were vaccinated was straightforward, but some people were presenting spurious exemption letters.
"We're seeing quite a number of medical exemptions and in some instances being provided by osteopaths, homeopaths, some doctors that are publicly seen to be anti-vax, we've had physiotherapists and in one instance a midwife issue vaccine exemption certificates," he said.
Rush said the letters were causing confusion.
He said principals were not medical experts so they needed explicit instructions from officials so they knew what they could and could not accept as a valid exemption.
The Education Ministry strongly advised schools and early learning services not to accept any medical exemptions until it and the Health Ministry had published further advice later this week.
Te Rito Maioha Early Childhood New Zealand chief executive Kathy Wolfe told RNZ it had received only a few queries from its members about "resistors".
"There has not been a significant issue across our membership in ensuring their staff have at least their first dose of the vaccination by 15 November," she said.