Last Wednesday was the eighth pay period since the organisation picked up the contract.
"In my view it has gone from just being annoying and inconvenient to incompetence and negligence," Mr Walsh said.
After being assured by Novopay the problems would be fixed by now, it was clear the payroll issues would in fact continue well into 2013, he said.
Even communication with Novopay was difficult.
"When we went on their website to register a complaint as they asked us to, we found the website was down."
Mr Walsh, the current New Zealand Secondary Principals' Association president, said the organisation had billed Novopay for the extra work done by school executive officers.
If problems were not fixed by early 2013 that bill would increase into the hundreds of thousands of dollars.
John Paul College alone had billed Novopay for $3000, he said.
Rotorua Principals' Association president and Mokoia Intermediate principal Deborah Epp said a lot of schools in Rotorua, including Mokoia, also had trouble with last week's pay period.
She said the recent problems for schools were mainly connected to support staff payments.
"It is interesting that the ministry has sent schools ... an email address and phone number to contact Novopay if they have any problems with their pay during the Christmas period.
"It is good on the one hand but also concerning that they are expecting something to go wrong."
Attempts to contact Novopay were unsuccessful.
On December 10 Novopay released a statement on their website which said they were experiencing a high volume of calls, so unfortunately it would take longer to get through.