Otago Primary Principals' Association president Brent Caldwell said many of the errors from the first pay run had been rectified and most staff had been paid correctly.
"Schools are reporting that while there are some outstanding unresolved issues, the number has declined.
"It is hoped the next pay run will see continued improvements all round."
However, one major concern remained, he said.
"The Staffing Usage and Expenditure Reports which indicate to schools the funds to be direct debited from school bank accounts have not matched.
"One school reports having had a total of $1700 removed in the last two pay periods, over and above the data sent to the school via the SUE report."
He said schools were now having to spend extra time tracking payments and direct debits from their accounts.
"It is disconcerting for school administration staff, not knowing how much money needs to be in the account to allow for these unexpected extra debits.
"The Otago Primary Principals' Association has been in direct contact with Novopay to bring this to their attention."
Mr Caldwell said Novopay had advised the majority of issues should be "tidied up" in the next pay period, and it was providing more in-service help for its own staff so they would be better able to respond to schools' inquiries.
"While some of the extra changes Novopay has made will correct issues, improve efficiency and systems, the increased workload for administration staff still needs to be addressed.
"The ministry have discounted any extra funding to offset the hours and hours of work generated by this changeover," he said.
"Another area of concern in the longer term is for administration staff hours, as Novopay has seen many payroll tasks passed on to schools directly.
"This will mean more time being spent on payroll duties than under the previous system," he said.
