The Principals' Federation says the latest Novopay pay round has left at least 400 teachers unpaid.
The school payroll system, worth $100 million over 10 years, has been plagued with thousands of errors since it was introduced in August last year, with underpayments, overpayments or no payments at all to some teaching staff.
The federation says the full extent of the problems will be clearer in a few days after a fortnightly survey is completed.
President Philip Harding says he is becoming despondent, because he knows how much work the latest problems will mean for teachers.
Mr Harding says Novopay is turning into a nightmare and principals have told him that they believe problems are snowballing, with errors on top of errors.
A Christchurch principal says he has four new staff members who were not been paid in either of the last two pay cycles.
Paul Wilkinson from Fairville School says despite filling out the correct paperwork and being told the staff were entered into the system, none have been paid.
Mr Wilkinson says he has had to write out cheques for those teachers, with Novopay and Ministry of Education staff told him to guess the correct amount.
"Frustrating is not a strong enough word to describe the level of stress that it is causing us. The only word that I can use is incompetent."
Mr Wilkinson says the teachers have done the work and deserve to be paid.