More than 1600 school staff in the first pay period of the new financial year were overpaid because of a new glitch introduced into the Novopay system while and old one was being fixed, at a cost of $90,000.
It is the largest overpayment seen through the Novopay payroll system since PricewaterhouseCoopers has been handling the data.
Minister Responsible for Novopay Steven Joyce released the latest pay roll data from PwC, which showed 16 per cent of schools had staff overpaid in the first pay round of the new financial year.
"As part of the remediation work to fix bugs in the Novopay system, a new error was made during a configuration change that meant when the pay went through it triggered an overpayment change that meant when the pay went through it triggered an overpayment of voluntary bonding payments to 1480 school employees totalling $92,323.''
The latest figures show 39 staff were not paid, 1647 were overpaid, and 206 underpaid - affecting 286 schools.
Mr Joyce said the mistake was a reminder of the challenges in remediation a very complex pay system.
"I am advised that it was a one-off event that has been corrected.''
Previous pay periods:
Pay period 26 - pay complaints received from 0.43 per cent of staff and 232 schools.
Pay period 25 - pay complaints received from 1 per cent of staff and 406 schools.
Pay period 24 - pay complaints received from 1.9 per cent of staff and 447 schools.
Pay period 23 - pay complaints received from 2.2 per cent of staff and 628 schools.