The Ministry of Education has confirmed 5000 staff have been underpaid and 15 not at all in the first run of the new school payroll system, but says the errors were just "teething problems".
The new computer payroll system, Novopay, was launched at the end of August and the first payments went out on Wednesday.
The $30 million system processes the pay of 90,000 school staff, is the biggest in Australasia and took three year of planning.
The ministry said those who were underpaid would be paid by today and the errors were just "teething problems''.
Secondary Principals' Association president Patrick Walsh said he would meet with the Minister of Education later today to discuss the problems with the system.