A new $29.4 million payroll service for the country's education staff has caused problems at Nelson schools, with some staff missing out on their pay this week and principals feeling frustrated.

A new Novopay payroll service was rolled out by the Education Ministry a fortnight ago, replacing a decade old system that some referred to as "a dog".

About 90,000 staff around the country are paid using the system, but principals around the country are concerned that not all will receive their pay tomorrow, including some in Nelson.

Nelson Central School principal Paul Potaka said he thought six of his staff would not be paid this week.

The staff had been on the transaction list to be paid last week, but as far as he could tell they would not receive their pay. Three staff would not receive allowances owed to them.

"Our biggest concern is for staff who have made financial commitments on the assumption they would be paid correctly and on time. It is clear that isn't going to happen this week," he said.

If staff were not paid by the system, the school would write a cheque to cover their wages until the payroll was fixed.

The period leading up to the changeover to the new system had been problematic and involved staff taking many hours to train, check, and troubleshoot, and training arrangements and tools had been far from satisfactory.

"Access to websites have not been ready in time, passwords have been found to be invalid or not working for some unknown reason."

Communication with ministry staff responsible had involved long periods of being put on hold, he said.

Clifton Terrace School principal Rob Wemyss said the introduction of the new system had not gone well, and although he had not had a chance to look at the relevant reports, he did not expect things to be in order.

"I suspect that a whole lot of people haven't been paid from the information I have been receiving from Novopay."

While he was sure the staff were doing their best, he had struggled to get through to any support staff when there were errors, he said.

"When it's all up and running it will work very well [but] they have gone into it half-cocked."

The move should have been researched better, he said.

"You can't muck around with people's pay, you get people knocking on your door asking, ‘where's the pay?"'

Hampden Street School principal Don McLean said he had only seen one glitch in his payroll, with one teacher accidentally put down to receive five days' pay rather than one day, but he had alerted the authority and was confident it would be fixed by the time the pay went out.

It was always going to be a tough job to deal with one of the largest payrolls in the country, but the transition was not insurmountable, and it had to be better than the old payroll system, "which was a dog", he said.

Education Ministry chief information officer Leanne Gibson said yesterday there had been issues with the implementation of the service.

"We acknowledge that this first pay period in Novopay has been challenging for some schools," she said.

"Novopay has put New Zealand's biggest payroll online and there is inevitably some fine tuning to be done."

The pay centre had to extend its processing hours for the latest pay period to make sure all timesheets were received.

The service will cost $12.5m a year until 2018 but Ms Gibson said it was free to schools.

- © Fairfax NZ News