Official figures for the last Novopay pay period show 39 teaching staff were not paid, 206 were underpaid and more than 1640 were paid too much.
The pay, which went out on Wednesday 4 April went to 942 more staff than the previous pay period.
The minister responsible for Novopay, Steven Joyce, says the increase in overpayments was primarily caused by a single software error and led to a disappointing overall result compared to recent positive progress.
He says the mistake is a reminder of the challenges in remediating a very complex pay system and he has been advised that it was a one-off event that has been corrected.
