The Principals Federation and the Ministry of Education are at odds over the number of mistakes in the latest payment under the new payroll system.
The Novopay system has been dogged by errors since it was introduced two months ago, with many staff underpaid, overpaid or not paid at all.
The Ministry of Education says it is aware of fewer than 60 people who were underpaid or not paid at all in this week, but the federation says nearly 700 schools have reported errors.
The federation's figure comes from a survey of principals, 79% of whom said one or more of their staff was not paid correctly on Wednesday.
Of the 873 principals who responded, 90% said mistakes made on previous pay days have not yet been corrected and 86% were not confident problems with the system will be fixed before the end of the school year.
The ministry said more than 87,000 people were paid on Wednesday and the number of mistakes has been falling with each pay period.