Mr Newman described the still uncorrected errors as "basic stuff", such as figures on bank statements being different to figures schools have received from the MoE. Mainly relief teaching staff have been affected.
The system's failures are also preventing principals from submitting next year's staffing budget, yet the MoE requires the figures to be in this month, Mr Newman said.
He believes the Novopay programme was adopted without an implementation plan. "They say they had key delivery milestones ... but there was no plan, no training, no trial - then how did they meet their key delivery milestones?"
The MoE has admitted the problems are the system itself.
Rebecca Elvy, Novopay business manager, said the ministry appreciates schools' perseverance while the payroll failings are being addressed.
"We've dramatically reduced waiting times at the call centre. We've developed a way for relief teachers to follow up their pay issues without needing to go through the various schools they work for. We've made substantial fixes to the reports schools use to verify their payroll - and we're continuing to work towards a 100 per cent fix on that issue," Ms Elvy said.
NZEI Te Riu Roa national secretary Paul Goulter said the amount the MoE should pay schools in compensation will run into millions of dollars.
"[This] has resulted in literally thousands of wasted hours across the country and has been taking attention away from important things such as teaching and learning," Mr Goulter said.
"The Ministry has had two months to sort the problems out. It is clearly not doing enough and downplaying the problems."