That's why the ministry stepped up its training and information programmes. And why I and others stepped in to help. The more direct assistance we can give, the better the outcome for schools.
I have just spent the past two weeks travelling around the country taking part in the ministry's training road-shows. More than 2200 school staff attended, representing about half of New Zealand schools.
On the whole, participants were grateful for the opportunity to be able to ask questions and get some answers to take back to their school. They won't become experts overnight, but we made steps forward in explaining the system.
These sessions have now ended, but up to 10 specialist case managers, including former school principals, senior staff and payroll administrators, are available to work directly with schools managing any further issues that may arise.
The sheer size and complexity of the system was always going to make the introduction of Novopay a challenge.
There are about 2500 schools in New Zealand, and therefore 2500 separate employers - boards of trustees.
Permanent staff in schools are, in the main, being paid on time and accurately through Novopay. It's for those staff who use timesheets where things have been challenging.
Everybody I work with recognises that fact and understands the difficulties. Add to that the fact there are 15 separate collective agreements embedded in the software and you add a great deal more complexity. But these early difficulties should not distract us from the benefits. Novopay will be an accurate and efficient online payroll service. Schools will have immediate access to their own payroll information.
There will be a computerised record of all transactions, making the system safer and more transparent.
And yes, Novopay will save schools time. Almost every transaction will be done at the touch of a button rather than filling out forms, and crucially schools will have more time to concentrate on other duties.
Once we have ironed out these transitional issues, I am convinced Novopay will be an effective, modern system.
I am glad Novopay was introduced in my school and I am pleased I have been involved in a project that I know will deliver real benefits over the longer term.
Geoff O'Halloran is deputy principal of Tawa College.