The Auditor-General's Office expects huge delays as schools try to complete their financial accounts after having to cope with the Novopay payroll system.
Thousands of teachers and support personnel have been wrongly paid or not paid at all in pay rounds over the past eight months.
School audits director Graham Potter told Parliament's Education and Science Select Committee the records this year will be far more complex to sign off than ever before.
He said the office is working with schools to minimise the cost of checking that the records are accurate.
School unions are still calling for the Novopay system to be scrapped, despite an announcement it will be kept for now.
The Minister responsible for Novopay, Steven Joyce, says the ministry will stick with it as some progress is being made.
However, new problems manifest themselves as changes are made to the software.
Principals Federation president Philip Harding said he hopes the Government will come up with an alternative solution that is not a 'lemon' and can be relied on.
Auckland Primary Principals' Association former president Jill Corkin said she has seen no evidence that the system has improved and hopes a new system will be developed.
She said morale among teachers has continued to drop because of the unresolved problems with Novopay.