School principals say Novopay is still struggling to pay teachers properly, with an average of almost six teachers at every school affected by incorrect payments.
A survey this week of 714 principals, conducted by the Principals' Federation, found 72.7 per cent of principals had no confidence the system was on track to becoming an effective payroll tool.
It also found an average of 5.89 staff per school were paid incorrectly in the latest pay round, while two thirds of schools still had unresolved problems from last year.
Principals' Federation president Philip Harding said he expected the first pay round of the year to be challenging, but the error rate was "way beyond anything we imagined".
He was also disappointed by the number of problems that remained unresolved from last year.
"We cannot ignore this direct feedback from schools, which tells us that the Novopay saga is far from over."
Earlier this week, Novopay Minister Steven Joyce said 0.69 per cent of staff complained about the latest payroll period on February 5. He said 234 staff were not paid, 107 were overpaid, and 175 underpaid. That was higher than the acceptable error level defined by the Novopay technical review last year.
"Early indications are that there was no particular software error that caused the non-payments. It appears at this stage to be due to a range of data entry errors."
Mr Joyce said the result underlined the high level of complexity as school years changed over, and considerable administrative changes needed to be made.