The Public Service Association says the ministry is planning to cut the number of staff in the unit from 23 to 14, in documents it has seen.
The ministry says it needs to review the unit because of the move to the new Novopay system, but there will be no job cuts until next year.
It says it has doubled the number of staff in the payroll unit to help with implementation of Novopay.
The school payroll is the largest in the country, with 92,000 employees. It has been beset by problems since the Novopay system began in September, with many schools' staff underpaid or not paid at all.
PSA national secretary Brenda Pilott says proposing a restructure now is irresponsible and insensitive, when staff are working hard to get Novopay running smoothly.