The Auditor-General says problems with school payroll system Novopay added more than $1.5 million to the cost of audits of school accounts in 2013 and delayed the process by months.
Lyn Provost on Wednesday published results of her office's audits.
The report says the Ministry of Education covered the additional audit fees, which were on top of the $10.5 million that schools paid.
It says complications caused by Novopay delayed the audits to the extent that only 31 percent were complete by the statutory deadline of 31 May compared with 95 percent the previous year.
The report says this year the ministry has provided information about six weeks later than planned, which is likely to delay the completion of the 2013 audits.