The Ministry of Education has acknowledged there were an unacceptable number of problems witha new system last week.
School principals say the Novopay system paid some staff too much holiday pay, others were paid too little and 5000 were not paid at all.
The ministry said the number of calls to the service centre greatly exceeded expectations.
Chief information officer Leanne Gibson said the number of calls to the service centre greatly exceeded expectations.
Ms Gibson said the ministry is disappointed the steady progress that had been occuring over the last few pay cycles has been affected by the problems.
She said 40 mistakes were made in the last pay round and those people were paid manually.
Holiday pay has also gone through, although a day late in some cases.
Despite last week's payroll difficulties, 92,000 people received their normal pay and the majority of those due their holiday pay also received it.
Ministry staff will be available this Friday to immediately make payments manually if there are any problems.