Ministry of Education chief executive Lesley Longstone says problems with a new school payroll system could stretch for the first year of the rollout.
Novopay has delivered the wrong pay to school employees since it was introduced three months ago.
Mrs Longstone told Radio New Zealand's Nine to Noon programme on Friday that problems with the parts which have been rolled out should be fixed by the end of the year.
She said new parts of the system will be introduced in the months ahead and that could create additional issues.
But Mrs Longstone said she is confident that schools will start to see the benefits soon.