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The Ministry of Education has promised to reimburse schools for the extra costs they incurred sorting out problems caused by its new Novopay system.
There have been about 8000 mispayments since the $30 million teachers' pay system was introduced in August.
The ministry said in a statement today that 8000 transactions from Novopay's early pay periods had now been cleared, and schools would also be reimbursed for additional audit costs related to the new system.
"We recognise errors in Novopay's staffing and payroll reports could create extra auditing work and therefore costs to schools as part of their annual financial audit," group manager Rebecca Elvy said.
"We are working with the Office of the Auditor General to first minimise the additional audit costs as much as possible. Any costs that schools have to incur, and that are directly related to Novopay, will be reimbursed."
A ministry spokesman said it was too soon to say how much it would cost to reimburse schools.
Meanwhile, the Secretary for Education Lesley Longstone said a specialist team had been set up to call every school and ask them about their problems with Novopay.
Ms Longstone said it had been very disappointing to have so many problems with the new system.
"I know a number of school staff and payroll administrators have been frustrated trying to work through them and we have shared that frustration."
The ministry said it remained committed to Novopay, despite vehement criticism of the new system.