Schools are paying teachers out of their own operations funding after ongoing problems with the Education Ministry's new payroll system, Labour claims.

In Parliament today, Labour's education spokeswoman Nanaia Mahuta highlighted the case of a teacher at Pomaria School in Henderson who returned from maternity leave.

She had received full pay for the first and second pay periods but her third and fourth pays were skipped, leaving her $2000 underpaid and having to borrow money from the school's operational funding to pay her mortgage.

The Ministry of Education has confirmed that in the last pay cycle of the $29 million Novopay payroll system, introduced in August, up to 100 teachers were either not paid or underpaid.


Associate Education Minister Craig Foss also confirmed during question time today that that 390 teachers had been overpaid.

He said 41 teaching or support staff had received advances and 23 had indicated they were willing to wait to be paid in the next fortnightly pay cycle.

When questioned by Ms Mahuta on the total amount of outstanding pay, Mr Foss said that information was not available under the Novopay system.

"Every non-payment or under-payment brought to the attention of the ministry if being addressed," he said.

Mr Foss would not say how long it would take for the problems with the system to be resolved.

Secretary for Education Lesley Longstone said extra staff were working at the Novopay call centre and on data entry.

Novopay experts were also visiting schools to assist principals and payroll administrators.

"Specialist training sessions will be offered for all schools to assist with end-of-year pay-cycle processes," she said.

"The Novopay system is paying the vast majority of staff correctly, However, the ministry acknowledges there are issues that must be addressed."

A survey by the New Zealand Principal's Federation found around 90 per cent of principals had unresolved problems with the last pay cycle.

Half of the 2400 principals contacted responded to the survey.

It found 86 per cent did not have confidence the problems would be resolved by the end of the year.