"We used to be able to do the payroll in one day. Now it takes several.
"There's thousands of people that aren't being paid correctly.
"If this was a normal workplace, the boss would be taken to court," he said.
Macandrew Bay School principal Bernadette Newlands said she, too, had spent a lot of time sending emails to Novopay to sort out incorrect pay issues.
It was a nuisance and the lack of action from the Ministry of Education was concerning, she said.
"Every time something new happens, you're waiting with bated breath to see if people are correctly paid, and you're not feeling confident that they will be."
Both Otago schools said they were trying to deal with former and part-time staff members who had been overpaid by $600 each.
They are among 581 people nationwide who have been paid on behalf of schools they have not worked at, and $560,000 has been advanced by schools themselves to cover Novopay's mistakes, figures released by the Ministry of Education this week show.
The figures also show 7899 people have been underpaid or not paid at all, more than 6000 people have been overpaid and only 281 manual payments to correct faults have been processed since Novopay started.
People trying to get through to the Novopay service centre were waiting up to an hour and a-half, 15,000 calls going unanswered or being abandoned altogether.
Mr Hayward was upset he and many other principals and support staff were still at school working through the issues while "the education minister is away happily on holidays".
NZEI national secretary Paul Goulter said the summer holiday period would normally be the most straightforward pay period of the year because it was the one time that no relievers and support staff were on the payroll.
"But the issues around Novopay are so massive and entrenched that principals believe they have no choice but to return to schools to deal with the expected fallout from yet another error-ridden pay period," he said.
"New errors develop every fortnight and there's nothing to indicate that this pay period will be any different.
"The week prior to Christmas was a total shambles despite the Ministry of Education downplaying the problems.
"It was enormously stressful for principals and school administrators at a very busy time.
"Now principals are being forced to come in early from their break to deal with expected new problems."
Mr Goulter said the most concerning issue was that the unacceptable level of stress for staff caused by Novopay was expected to continue into the new school year.