Some beginner teachers are being underpaid around $20,000 a year, putting their salary below the minimum wage.
The Ministry of Education says there are 661 teacher cases of underpaying that need to be processed, in addition to 2000 being overpaid.
One Auckland teacher said his school loaned him $1000 for basic needs.
"It makes me feel a bit isolated," the teacher, only known as Josh, told Newshub.
"I haven't been to a single gathering, because I can't afford it. I can't go out with my friends on the weekend if they're doing activities that will pile up the money."
Josh says he struggles to pay for fuel and equipment for the classroom, and can't imagine how anyone would make ends meet if they were paying a mortgage.
"I'm flatting at the moment and I'm struggling. My weekly rent is $180, and I come out at the end of the week with a few dollars, if I'm lucky."
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The Ministry of Education says underpaid teachers will receive the backpay they are entitled to, with the 661 salary assessment requests expected to take three weeks to process.
The underpayments are the result of salary assessments not being completed, TVNZ reported. Many are on rates that are below the new minimum wage, which kicked in this week.
But Josh said a friend of his took two years to get her money, and they're not allowed to contact Novopay directly to ask when theirs will be ready.
The underpayments come at the same time Novopay is demanding teachers who have been overpaid give the money back.
Novopay has been causing issues since it was first rolled out in 2012. Tens of millions of dollars was spent fixing it, but issues clearly remain.