Some Masterton teachers fear worse payroll woes to come, said Solway Primary School principal Gail Marshall.
Mrs Marshall said the last two Novopay payment rounds were flawed for a handful of her teachers during the holiday break and she is expecting problems to worsen during the first pay round of the new school year in early February.
"I'm holding my breath about that pay. There will be new staff and new contracts and the system won't be able to handle just the changeover let alone any errors we make. You can guarantee that pay will be messed up. It will be chaos," Mrs Marshall predicted.
Novopay has been wracked with problems since its launch in August and the NZ Secondary Schools Principals' Federation has written to the Auditor-General asking for an urgent review of the system.
Mrs Marshall said two of her full-time teachers had received only half of their pays during the seasonal break and the school was funding the shortfall.
She said Solway is today running "at a bit of a deficit" because of the unbudgeted payments, but still has savings in reserve, unlike some other schools.
The Ministry of Education would provide financial support to schools "disadvantaged by overpayments" made from their operations grants, said ministry group manager Rebecca Elvy.
Ms Elvy said a ministry team had been "working closely with schools and the sector over issues with Novopay and are aware of this particular concern arising from overpayments to some staff".
"We understand some schools are worried this is putting pressure on their bank accounts and I want to assure them that we are working on this as a real priority and that we will support them while we correct the problems."
Ms Elvy said the ministry is also working with schools to assist them with the start of year process which needs to be completed by Monday.
"The start of year process involves re-starting staff on the payroll for the beginning of the school year. A team is working with principals and school administrators to assist them to complete the start-of-year process."