The Ministry of Education says only a handful of teachers did not receive their full pay in the latest glitch with the new payroll system.
The ministry says the $30 million Novopay system paid 90,000 school personnel this week and fewer than 100 had a problem.
A high school teacher in Dunedin told Radio New Zealand News she was one of 11 people underpaid at the school and that one teacher had not been paid at all since the system was introduced six weeks ago.
Secondary Schools Association president Patrick Walsh said that if the system is not fixed shortly, there will be calls for it to be scrapped.
He said the patience of school staff is wearing thin, with many having to spend hours every week on Novopay problems.