Bay school staff have been overpaid more than $600,000 in the Novopay debacle.

Wrong payments have affected 631 local school staff since Novopay's introduction in 2012, with 86 staff underpaid and 545 overpaid, new figures show.

The amount underpaid was $151,175 and $639,574 had been overpaid. Almost half of this money, $301,818, had been paid back to the Ministry of Education.

A spokesman for the minister responsible for Novopay, Steven Joyce, said collecting the large number of outstanding overpayments remained a priority.

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"Overpayments in Tauranga and the Western Bay of Plenty are tracking at a similar rate to that of the national rate, with just under half of the overpayments repaid.

"We acknowledge that people have been overpaid through no fault of their own and that dealing with an overpayment can be frustrating. However, the money does need to be repaid. The ministry will continue to work with affected school staff and no one is being referred to debt collection agencies."

Otumoetai College acting principal Ricky Feutz said there were still problems with Novopay at the college, but it had improved.

So far this year, the school had 10 staff overpaid and five staff underpaid.

Although there were fewer problems, Mr Feutz said the school's payroll administrator had been working an extra seven hours a week to sort out issues associated with Novopay.

"We put that down to improvements from Novopay and more knowledge of the systems from people working here. There are still leave issues in relation to staff on annual leave or sick leave."

Brookfield School principal Robert Hyndman said the system was improving.

"It's less of an issue than it was last year but there is still stuff. Most pays are okay," he said.

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Teachers who had been overpaid in early 2102 had paid it back to the school quickly, but it was still proving difficult to have it rectified with the ministry, he said.

Kaka Street Special School principal Barrie Wickens said the school was now only dealing with one error per pay period.

"Sick leave entitlement seems to be a nationwide problem," he said.

While the system seemed to be working slightly better, educators were still doubtful, he said.

"There's no confidence among the education sector that they have got a system that's trustworthy and accurate," Mr Wickens said.

"At the moment they are getting things right but we're still not out of the woods."

Tauranga Boys' College principal Robert Mangan said overall Novopay had become more user-friendly but that was not to say it was perfect.

At the end of 2013, the college had eight people overpaid relating to the 2012 period. The largest overpayment was about $4000, Mr Mangan said.

"The end of year 2012 and start of year 2013 process was a real challenge. The system would not accept the entries and lost work that had been imported, and with the pressure of timelines ... Most pay periods there are errors, mostly minor."

Western Bay of Plenty PPTA chairman Graeme Bridge said Novopay was still causing issues.

Mr Bridge said the association was doing what it could to help those affected by overpayments and underpayments.

The spokesman said affected people were given repayment options and were encouraged to ask advice from their school's payroll administrator.

Nationally, as at March 30, there was a total of 17,374 overpayments in New Zealand worth $18.3 million since Novopay first began.

Latest data showed $9.4 million had been repaid, with the current repayment rate of about $1 million a month. The Education Ministry wrote-off $156,000 of debts worth less than $100.