Principals are threatening to hold a vote of no-confidence in the Novopay payroll system.
The $30 million system developed by Australian company Talent2 has been plagued with thousands errors since it was introduced in August 2012 with underpayments, overpayments or no payments at all to some staff.
Secondary Principals' Association president Patrick Walsh said on Wednesday yet more problems are being reported and though the number of errors is lower than last year, he expects the volume to shoot up when the school year begins next week.
In addition, Mr Walsh says some pay problems logged with Novopay last year have still to be resolved, leaving some staff still waiting for wages they should have received in 2012.
He says they have also discovered inherent problems with the system that will increase the workload for staff - even if all the problems with it are fixed.
In a Cabinet reshuffle announced on Tuesday, Economic Development Minister Steven Joyce was put in charge of sorting the problems out as soon as possible.
Mr Walsh told Radio New Zealand's Checkpoint programme the vote is intended to show the minister that schools have no confidence in the system and is calling on the Auditor-General to investigate and decide whether it should be scrapped entirely.
"We still are waiting for the inquiry which was scheduled for April - we think that's far too long.
"We would prefer the Auditor-General to investigate Novopay so we can actually have the books opened and see how extensive the problems are, and whether in fact we remain with Novopay or go to a system that actually will work."
Novopay bungles have cost schools hundreds of thousands of dollars in extra administration work, which will need to be reimbursed by the Government, he says.
The Auckland Primary Principals' Association says it believes Steven Joyce has the skill and experience to resolve the problems.
However, it says it is frustrating it has taken so long to get proper leadership, given it was clear months ago that there were serious problems with the system.
The association says it hopes Mr Joyce will focus on fixing Novopay, rather than finding who is responsible for the errors.