OPPA president Brent Caldwell said the ministry and Talent 2, the company which designed and runs Novopay, had acknowledged the system had design errors and they were taking ownership of the problems.
"But, for the moment, their priority is on getting the system right."
Mr Caldwell said OPPA executive members met the Ministry of Education's chief information officer Leanne Gibson and compliance/reporting manager John Warner and Talent 2 chief executive Brian Ashton in Dunedin yesterday to discuss specific examples of issues faced by Otago schools.
The issues were shared and noted by the ministry and Talent 2, he said.
"They are taking heed of the suggestions from the sector and are making changes to ensure each pay period is more accurate, while simultaneously addressing the huge backlog of almost 8000 issues."
Mr Caldwell said the ministry officials also accepted face-to-face training on how to use the system was "far superior" to the web-based training provided.
So the ministry has planned a nationwide roadshow for November which will focus on end-of-year and start-of-year payroll instructions.
"Talent 2 and the ministry have used a testing strategy to ensure these two crucial staffing and payroll rounds are error-free.
"Roadshow attendees will also have an opportunity to discuss other issues."
Mr Caldwell said there were also reassurances on possible issues with school audits.
The ministry had briefed the Office of the Auditor-general, and the Auditor-general would give instructions to school auditors regarding staff usage and expenditure reports.
One of the main points of discussion concerned the impact of late mortgage, IRD or loan payments for school staff who had not been paid properly as a result of Novopay problems.
Mr Caldwell said the ministry confirmed it was taking responsibility for any fiscal penalties incurred by employees because of late payments.
School administrators would have to contact the Novopay Service Centre to action this on behalf of employees, he said.