The Auditor-General has announced it is monitoring the problems with the Novopay system, but it is not investigating the Ministry of Education's payroll system at this stage.
The system, which handles the pay of school staff, has been plagued with errors since it was introduced in August last year, with staff not getting paid the correct amount or not being paid at all.
Auditor-General Lyn Provost said the office would consider investigating the issue should the ministry fail to fix the problems with the system.
"Our current priorities around Novopay are completing annual audit work to ensure that schools are able to sign off their payroll reports and their annual financial statements," Auditor-General Lyn Provost said in a statement.
"We appreciate that schools may be concerned at the potential for increased audit costs as a result of the Novopay problems. We are working with the Ministry to minimise the workload for schools on their 2012 financial statements, as well as minimising any additional work that auditors have to carry out," Mrs Provost said.