The head of the company behind the Novopay payroll system has apologised to school staff left unpaid before Christmas but says he's "bamboozled'' anyone would be in that position.

Chief executive of Australian company Talent2 John Rawlinson said there was no reason for staff to go unpaid because they could get cash advances from their individual schools who would be reimbursed.

"Either staff don't know about the process, the school doesn't follow the process or they just don't want to get paid - I agree you shouldn't have to worry about it, it should go into your bank account, but from day one there's been a process.''

Mr Rawlinson said there was a helpline and it would be staffed during the holidays to deal with problematic pay.


"At Talent2 we have a mantra that we want to be a force of betterment for people; and individuals that work in those organisations.''

Mr Rawlinson echoed the comments made by former Secretary for Education Lesley Longstone, saying if he could go back and roll out Novopay differently he would - but he wouldn't think twice about accepting the contract.

"We're really sorry that it hasn't gone better. It's been new and there have been some errors, and there have been parts of the process that haven't worked as well as they should have and for that we apologise.''

Schools have been left reeling at the beginning of their holidays after a last-minute scramble to try to stop incorrect payments from leaving school bank accounts on Thursday night.

There have been significant problems with holiday pay. Staff reportedly faced wait-times of more than 30 minutes when they tried to get through to the Ministry of Education's helpdesk.

The ministry's chief information officer Leanne Gibson said 300 school staff had not received their holiday pay, but 73,000 school staff received their final pay for the year.

Ilminister Intermediate School principal Peter Ferris tried to sort out $10,000 that had been wrongly allocated to be paid to former staff. He was unable to, and payments of $5800 went to one staff member who hadn't worked at the school for six months, and another $3600 went to a former part-time cleaner.

He tried to contact the ministry's helpline on Thursday but the payment still went through.

Mr Ferris said the school had problems in all pay cycles since August and the Ministry were yet to reimburse the school $3500.

Thousands of staff have been incorrectly paid since the $30 million Novopay system for 92,000 school staff was introduced in August.