Principals say they have not been given enough time to prepare for end of year of pay complications using a new school payroll system.
There have been several complaints about the Novopay system since its introduction on 5 September this year, including staff being underpaid or not paid at all.
Training sessions in how to use Novopay to sign up new staff and sign off those who are leaving start in Wellington on Friday and move to other centres next week.
But Novopay did not send an email alerting schools until nearly 5pm on Wednesday.
Principals say that is not enough warning, as they are in the middle of a busy time and now have to rearrange plans so key staff can attend.
Wellington's Sacred Heart College principal Lisl Prendergast says the lack of notice is unacceptable.
"Seniors do not leave here until Tuesday of next week, we have our big prize-giving on 5 November. All the other colleges would be the same.
"It's just an insane time of the year to be doing this sort of thing. It actually shows that people don't understand fundamentally where schools are at."
Ms Prendergast says the Novopay system is creating too much administrative work for schools.
The Ministry of Education has not responded to questions about the training sessions. It says 90,000 people were paid by Novopay on Wednesday and the ministry has been told that 221 people were underpaid or not paid.
However, Principals Federation spokesperson Peter Simpson said there were new errors, in which the pay of teachers and support staff has been changed for no reason. For example, one senior teacher's salary was down $170.
Mr Simpson said mistakes made in previous pay rounds had not been fixed.