"Every pay round there seems to be new errors occurring," the Mahora School principal said.
"We've still got staff who have been overpaid and underpaid."
The Novopay debacle was one of several issues, including proposals around bigger class sizes, charter schools and national standards, that caused tensions between teachers and the Education Ministry last year.
Mr Pearse said schools were dedicating too much time to fixing problems caused by the system.
"The disappointing fact is that there are just so many additional hours being put into this.
"[The] current track record suggests new errors just about every pay round. We want a stable system that works."
Novopay, which cost $30 million to develop, went live in August. As of January 9, education staff were owed almost $12 million, Official Information Act data reveals.
It also shows 225 invoices from schools and school support staff were sent to the ministry for $1.197 million in extra costs incurred administering Novopay errors.
Disagreements between system developer Talent2 and the ministry are also revealed.
Two months before Novopay was signed-off by the Government, Talent2 was told it was in contractual default for failing to meet roll-out targets. A breach notice was threatened, however Talent2 argued defects were acceptable for the state of the project.
Talent2 told the ministry to refrain from what it called excessive reviews and attempts to manage it on contract matters.
Minister in charge of Novopay Steven Joyce announced a ministerial inquiry and technical audit of the payroll system on Thursday.
Mr Joyce said a contingency plan was being investigated, which could include scrapping the system and replacing it with Datacom - the previous payroll provider.
However, disposing of Novopay would not be taken lightly.
"You would have to wind back a significant amount of what's been done and then go forward again, and I don't think anybody is under any illusion that that solution would be at least as painful as where we are in the short term."
New Zealand Educational Institute president Judith Nowotarski said schools had put in long hours sorting out the mess and wanted a deadline for when the system would be fixed.
"There may be a plan now but it's cold comfort to our members who are still suffering."
The Government has previously promised to compensate schools for time spent administering payroll errors.
Green Party education spokeswoman Catherine Delahunty said the system should never have been signed off with its high error rate. APNZ
