The president of the Secondary Principals' Association has called Novopay a "toxic brand" and believes it is in its death throes.
While schools were closed for Waitangi Day, many administrative staff worked to resolve more Novopay mistakes after another fraught pay round overnight.
One principal said 30 of her staff were either not paid, or incorrectly paid, while two others told ONE News that a third of their staff have unresolved pay issues.
Several schools reported calls from Ministry of Education officials telling them to ignore transaction reports because they are wrong again.
"It is becoming increasingly clear that whatever steps and options are taken, including the possibility of scraping Novopay and going with another provider, the 'mess and pain' will continue for some time," Patrick Walsh, the president of the Secondary Principals' Association, said.
"It is entirely regrettable that it has taken seven months to get concerted action. Given that our membership had a 95% vote of no confidence in Novopay, compensation is clearly needed in addition to the above to restore good will.
"It has become a toxic brand with even Minister Joyce, describing it as 'dog with fleas'. I think it is in its death throes and is more accurately described as a 'dead cat bouncing'."
Ministry of Education Group Manager, Rebecca Elvy, said the Ministry has been operating its call centre today for staff who have not received any pay or were underpaid significantly.
"As at 2pm today, the Ministry call centre had received 266 calls. Nearly all have been from individual school staff, with some also from principals and payroll administrators on behalf of their staff."
She said most calls have been about staff not being paid or being significantly underpaid
"The Ministry is processing 60 direct payments, which the major banks have agreed to pay into bank accounts today, notwithstanding it is a public holiday, and we're really grateful for their assistance. Direct payments can also be made, as usual, tomorrow."