Figures for the last Novopay pay period show 84 teaching staff were not paid, 173 were underpaid and 122 were paid too much.
The pay round, which went out on 20 March, paid 2623 more staff than the previous pay period.
The data comes as schools prepare to receive compensation of $6 million from the Government for the extra administrative work caused by the new payroll system.
The Minister responsible for Novopay, Steven Joyce, says the next pay round will be the first of the financial year, which may create more errors as it contains changes such as adjustments to KiwiSaver and student loan repayment rates.
Mr Joyce says pay teams are working hard to finish processing ahead of next week's pay and will be working over Easter weekend.