The Office of the Auditor General says it will work with the Ministry of Education to minimise the extra audit work caused by problems with the school payroll system.
Schools are worried their auditors will have to work a lot of extra hours to verify they have paid staff correctly.
The office says it will also work with the ministry to ensure schools are able to sign off their payroll reports and their annual financial statements, with confidence.
It says it is still assessing the effect of the payroll problems on school audits.
School principals say they are still finding errors in the school payroll, despite official assurances problems with the new system are being fixed.