Rotorua Lakes High School principal Bruce Walker said he felt for smaller schools who could not afford to cover staff salaries while their pay was being sorted out by Novopay.
"It is a shambles. We have teachers who were dependent on their pay to cover bills and mortgage payments. Luckily we are a big enough school to support those 10 or 15 staff but I don't know how smaller schools are faring."
He said once things had been ironed out he hoped Novopay would consider compensation for teachers who incurred bank fees and penalties.
Of the five schools The Daily Post talked to, all had been affected and had all struggled to get hold of anyone at Novopay to fix their problems.
Novopay's website asks affected schools to call or email it to sort out any issues, but John Paul College principal Patrick Walsh said despite their best efforts they could not reach anyone over the phone nor did they receive any replies to emails. He said he doubted Novopay would even have things sorted out by next Wednesday.
Mr Walsh said he could understand a few hiccups with a big payroll changeover but the current predicament was unexplainable.
"It is surprising they are having so much trouble when they had three years and $30 million to set it up."
He said examples of staff being disrupted by the changeover included a senior teacher on $70,000 being paid a $35,000 salary, several relievers being paid twice and others not paid at all.
Kaitao Middle School financial executive Donna Burns said one teacher's pay had "dropped off the face of the planet".
"On Tuesday [Novopay] sent out a news flash saying we had to go through and fix a whole lot of details on our end."
Mrs Burns said she spent half a day stressing and working hard to do what they said before getting another email apologising for the directions because, in fact, she did not need to do them at all.
Mrs Burns said their fortnightly draft pay slips were released on Thursday without any changes to the affected teacher's pay problem. After spending 47 minutes on the phone waiting for someone to pick up at Novopay, she gave up.
Novopay has released daily updates on its website to assist schools with the changeover issues. It reported that some details left off its draft pay report would be amended on Wednesday.
In one update, Ministry of Education chief information officer Leanne Gibson said it held an emergency board meeting to prioritise the key issues.
"This is a big, complex, distributed system that was always going to create some ructions at introduction - as has been experienced.
"We know that it has required significant input, commitment, pressure and associated stress from schools across the country for which we are extremely appreciative.
"The team is now working hard to ensure the second pay run is as close to humanly perfect as possible."
Attempts to contact Novopay were unsuccessful.
