The principal of Otumoetai College, the Western Bay's largest school, has only had about five days leave while the rest of his time had been spent dealing with Novopay issues.
Dave Randell told the Bay of Plenty Times that the school's finance manager, accountant and himself had tried to sort out multiple payment issues, including one support staff who was on sick leave and hadn't been paid for four weeks.
"He's had to have surgery ... and for the first four weeks of his sick leave he hasn't been paid. The poor man.
"We are dealing with people's lives. I don't care about the money or cost to the school, we're a large school so we can use our [operations] grant but not all schools can afford to do that."
Mr Randell said if he worked at any other work place, his employees could have taken him to court for breaching the teachers' agreement and not paying them.
He said the Novopay system was "an absolute shambles" and he was disgusted with the way it was being handled by the Ministry of Education.
"Every time there's a mistake you have to fill in lots of forms and action sheets. We're just going around in circles.
"I've come back to school early to help sort this mess and to support our teachers. I'm slacked off about how this has affected people. It's not just money, it's their lives. These people have mortgages, families and payments they have to keep and to have issues continuing is a joke. It's beyond a joke."
At Tauranga Intermediate, office staff returned to the school this week to work on Novopay payment inaccuracies, principal Brian Diver said.
Meanwhile at Mount Maunganui College, the first pay of the year, on Wednesday, revealed it was the first pay since August where staff hadn't been underpaid.
"No one has been underpaid which is excellent ... but there are still other issues," he said.
"We still have 40 outstanding pay issues since August that haven't been resolved. We're slowly working our way through these."
Mr Gordon said the school had proposed a New Year's resolution that would see every Novopay issue be sent to the Ministry of Education as well.
"It hasn't been handled very well so maybe this will make them realise we've had enough."
Teachers union NZEI said Novopay was contributing to an "unacceptable level of stress" for staff going into the new school year.
The Ministry of Education yesterday announced it would provide financial support to schools disadvantaged by overpayments from their operations grants.
It was earlier revealed schools around the country had stumped up more than $560,000 in advances to teachers and support staff whose payments were botched between August and November last year.