He said some former staff members were still being paid from Carlton School, even though they had left the school last term.
"Then we have to jump through hoops to try and get the money back. Some of these people are not very familiar with where their money is coming from and they spend it."
Mr Petersen said the school's relief staff had simply not been paid since Novopay was introduced, and others were having problems when their salary needed to be assessed.
He said while Novopay was supposed to make staff pay easier, it had had the opposite effect.
"It's actually loaded a huge amount of work back on to the school. There are endless forms to fill out - the amount of paperwork is unbelievable," Mr Petersen said.
Tawhero School executive secretary Sandra Carrick said she was dealing with a variety of pay issues among the school's 61 staff members.
Ms Carrick said dealing with Novopay took up so much of her working day that she had to take her regular work home and catch up with it in the evening.
"I used to spend about half an hour a week on payroll - now I am working up to eight hours a day some days trying to fix their blunders. I am one of the hundreds of administrators that are fed up to the back teeth and beyond with all the Novopay blunders."
She said glitches at Tawhero School included staff being overpaid or underpaid, being paid at the wrong rate, allowances, medical insurance and retirement contributions being cut, and staff not receiving pay slips.
"For one staff member I have been given 15 job numbers from Novopay, and the issue is still not resolved," Ms Carrick said.
New Zealand Education Institution (NZEI) spokeswoman Deborah Mannington said it was impossible to say how many schools in Wanganui had been affected by pay glitches, as the organisation - which represents primary and intermediate school teachers - had not been keeping statistics on the matter.
But she said anecdotally the NZEI knew schools throughout the country were still struggling to pay their staff correctly through Novopay. She said it was very frustrating for the staff involved.
In a survey conducted by the New Zealand Principals' Federation, 90 per cent of principals that responded said they had "on-going problems yet to be resolved from previous pay rounds". Some 86 per cent had no confidence their problems would be resolved by the end of the year.
The Secretary for Education, Lesley Longstone, said the Ministry of Education was committed to addressing the backlog of Novopay transactions, and thanked school staff for their patience during the payroll transition. "The ministry accepts there have been teething issues moving to a new system and a lot of work is being done to resolve issues that have emerged since implementation."
She said the system had been paying the majority of staff correctly.
Novopay glitches - some of the faults have been fixed.
Timesheets or leave bookings for staff with apostrophes in their names [eg, O'Brien, Fa'alili] cannot be entered into the Novopay system;
An employee with a long or hyphenated name will show up on the payroll as an additional staff member;
Sick leave not showing up against a teacher's name;
Extra hours for part-time staff cannot be entered into the system;
Leave balances for staff may be displayed incorrectly.