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Both of the teachers unions - NZEI and the PPTA - have confirmed they will be taking legal action against Novopay.
They have been told by Novopay the new rates and backpay for union members, which took effect from July 1, will not be paid until September 11.
Representatives from the unions have said they are talking to lawyers about their options.
Education Minister Chris Hipkins tweeted last night the delay was not good enough and said he would be following the matter up.
Today however, the minister said the delay was unavoidable.
"I reluctantly accept that the complexity of implementing a unified pay scale and making significant changes to the agreement is going to result in a delay in implementation."
Mr Hipkins said it was frustrating and if there was a way to speed up the process he would.
In the meantime, he said the replacement of Novopay was under way.
Since teachers heard about the delay, both unions have said they would take legal action against Novopay.
Primary school teachers union NZEI national secretary Paul Goulter said it was outrageous teachers had to wait so long.
"We will move everything we can, to ensure those teachers will get what they're entitled to when they're entitled to it," he said.
The PPTA said it was prepared to keep pushing legal action against Novopay even after pay increases won by teachers were paid out.
PPTA vice president Melanie Webber said the reasons for the delay were unacceptable.
"It's more than possible that the legal action won't be concluded by that time but what we need to do is send a clear signal to people that this is unacceptable. You cannot wait over two months to give people the pay increase that you have promised them."
Ms Webber said teachers were expecting that money, and were facing financial burden as a result.
National's education spokesperson Nikki Kaye said all resources needed to be put in to getting teachers paid urgently.
"Some teachers are messaging me saying how is it that it only took them two pay cycles to deduct the strike action, but it's going to take them five pay cycles to actually pay them their pay rises," she said.
Ms Kaye said the Government prolonged negotiations for over a year for secondary teachers, so the Ministry of Education and Education Payroll had a long time to prepare.
"The reality is there are tens of thousands of teachers with bills to pay and mortgages that need the minister and agencies to deal with this matter urgently," she said.
Education Payroll, which is in charge of Novopay, sent a written response in which it said it had never before faced a payroll adjustment of this complexity.
In the statement, chief executive Arlene White said teachers often had multiple roles, so there were 139,000 individual jobs requiring pay adjustment.
Ms White said the current payroll system did not have the facility to easily make the complex adjustments required, so they were having to design, write and extensively test new code.
She said the replacement payroll service that Education Payroll was building, called EdPay, would allow considerably more flexibility and responsiveness to changes in the future.
A nationwide strike by primary, secondary and area school teachers over the pay deal that was on offer took place on 29 May, but teachers at primary and intermediate schools subsequently accepted a deal giving them an 18.5 percent pay rise over three years.
However, the deal was rejected by primary and intermediate principals who said the latest offer would have seen some principals in smaller schools paid less than some teachers in larger schools.