The Ministry of Education says it will consider paying schools for any extra audit costs caused by problems with its new school payroll system.
Principals say they cannot sign off their pay records because of the problems and fear auditors will charge thousands of dollars to check that the records are accurate.
There have been several complaints about the Novopay system since its introduction on 5 September this year, including staff being underpaid or not paid at all.
The ministry said on Tuesday it is doing everything it can to fix the problems and is meeting daily with the payroll provider, Talent-two, and is giving more support and training for schools.
It is also seeking to allay fears about audits, saying it will work with the Office of the Auditor-General to minimise the costs and compensate schools where appropriate.
The Principals Federation says that is good, but the ministry should go further and pay schools for the extra administrative and accounting work the payroll has caused.
Spokesperson Peter Simpson says principals' frustration with the payroll system is turning to anger.
The Auckland Primary Principals Association has called for a boycott on new work with the ministry until problems with Novopay are fixed.
The association acknowledges that will harm government policies, including the national standards in reading, writing and maths, but says its members are too busy with the payroll problems to take on anything else.
President Jill Corkin, of Snells Beach Primary School, says principals just want their staff to be paid correctly.
Meanwhile, the Education Ministry says most of the errors schools are reporting are not affecting people's pay.
Principals are reporting a much higher number of mistakes delivered by the Novopay system than the ministry has reported.
The ministry says it counts only errors that result in a missed payment, over-payment or under-payment. It says other mistakes might include information missing off a pay slip or an incorrect leave entitlement, which do not affect pay but are causing stress for schools.
The ministry says it is working hard to make sure Novopay works well for all schools and employees. It has given the company until 14 November to clear a backlog of more than 4000 errors remaining from Novopay's first two pay days.