Acting head of Education Infrastructure Service Jerome Sheppard said the ministry suspended debt collection in March 2013 but it "hasn't ruled out using debt collection to recover outstanding debt in the future".
He said the ministry had recouped about $16.8m in overpayments. About 1380 staff were making repayments - some as little as $5 a fortnight - to clear $3.1m.
Now the ministry was looking at recovering the final 10 per cent. It had previously wiped all overpayments under $100.
"We want it cleared as soon as possible," Sheppard said.
Staff would be expected to arrange regular repayments if they were unable to repay immediately.
Primary teachers union NZEI president Louise Green said the missing money showed "what an ongoing debacle Novopay continues to be".
PPTA president Angela Roberts said it continued to be "murky" and many teachers were suspicious about how overpayment figures were reached.
"There was often a lack of clarity about how Novopay calculated any potential shortfall or overpayment," she said.
Labour education spokesman Chris Hipkins said Novopay had been a fiasco from day one.