Otago Primary Principals' Association president Brent Caldwell said the letter, written on behalf of Otago's primary principals, outlined their concerns about the new system, and sought assurances they would be addressed.
Mr Caldwell said the computer system, designed to deliver the school payroll, was launched last week, but principals across the country were complaining they could not get through to the Novopay helpdesk, payroll information was incorrect, and their staff were having to spend more time on the payroll.
"The first draft - staff usage and expenditure (Sue) reports - was made available for downloading last Thursday.
"It quickly became apparent that Sue reports received by schools had many glaring errors when compared to each school's data input records."
Errors included teachers not being paid sick leave to which they were entitled, incorrect support staff payments, some support staff not appearing in the Sue report at all, and day relievers being grossly overpaid.
"In one case, a day reliever was paid $7600 for one day's work."
Unreasonable stress and anxiety had been created in schools by the data entry faults by Novopay staff, which was "inexcusable given the resources Novopay has had at its disposal", Mr Caldwell said.
"Administration teams in Otago schools, and their counterparts around the country, have spent a great deal of their own time training and reading up on the system in order to be adequately prepared to input their data correctly.
"It is extremely disappointing to have to act as quality control on a system that has been years and millions of taxpayer dollars in the making, especially as recent correspondence from Novopay highlighted their high standards and key performance indicators for their service."
A Ministry of Education spokeswoman said issues were still being ironed out of the system, but all would be well.
She said the ministry had increased the help offered to schools and assured principals their staff would be paid today..
