Novopay is a deeply flawed payroll system that is falling apart, says Lakeview School principal Ed Hodgkinson.
Mr Hodgkinson said errors persisted through the first pay round for the year on Wednesday with a teacher receiving payment for only five of the 14 days she had worked, overpayments going to several other workers, and the collapse of an online communication link with the payroll provider, he said.
"We're still having incredible issues with Novopay. I think we need to go back to scratch and start again. It's been a nightmare," Mr Hodgkinson said.
An example, he said, was the breakdown of a system of online forms that schools were to complete and submit to Novopay when a payroll error is discovered.
He said schools were able to call a hotline number to help resolve errors although there was a risk of "waiting on the phone for two hours to be finally given the wrong information".
Mr Hodgkinson said the previous payroll providers, Datacom, had successfully handled the job before Novopay was rolled out flaws and all in August 2012. "If Datacom can do it, let's move back to that," he said.
He applauded the school staff across the country who are enduring the defective system and fighting to make it work.
"I take my hat off to the teachers and support staff who are sticking in there despite having no confidence in Novopay at all. Workers in any other profession would have walked out way before now," Mr Hodgkinson said.
Greytown School principal Kevin Mackay said there had been three staff members who were not paid on Wednesday and another part-time teacher who was significantly overpaid.
He said the school also had outstanding payment errors from September that were still unresolved, including overpayment debt recovery that would not be started until May.
Mr Mackay believed Novopay should be dismantled "if they had something to replace it with", but said the Ministry of Education had been caught in a trap of its own making.
"It's horrendous but they've got nothing else, so they have to make it work," he said.