District health boards say that having to pay wage and salary arrears could have a significant financial impact on them.
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The boards and unions are at odds over how to run audits to figure out whether hospital staff have been underpaid for leave and shift allowances for years.
Other agencies and businesses face multimillion-dollar bills over payroll problems to do with the Holidays Act, which is under review.
Jim Green, a spokesperson for the country's 20 DHBs, said they had not sought assurances from the government over whether funding would be available to pay any arrears, which they have committed to pay back to 2010.
They had told the Health Ministry they would need to look at how to fund that.
"We've certainly made them aware about the fact that it may be a large sum that is involved," he said.
"If we do come out the end of the process and there are widespread issues, then that may have quite a financial impact on DHBs.
"So we've certainly kept them appraised about how this is shaping up but we haven't been able to give them anything definitive on what the impact is."
Unions said all the DHBs had underpaid staff and some were still underpaying them.
Health Minister David Clark Photo: RNZ / Rebekah Parsons-King
In addition, many DHBs were already in deficit so paying staff back could make that worse, said Deborah Powell, who represents 3500 junior doctors.
"They should have put the minister [David Clark] on notice that there's money [needed] here," Dr Powell said.
"If the minister is expecting the district health boards to pay these arrears out of operating budgets we will be in serious trouble. We will not be able to do it."
David Clark would not answer RNZ's questions about whether the government had or would set money aside for DHB arrears.
"The minister said he was not going to say anything while the DHBs and unions are still negotiating," Ms Powell said.
"I would have preferred to hear the minister say whatever the outcome, we will obviously be funding it. But he didn't say that."
RNZ has asked Treasury if it was setting aside any contingency for DHB liabilities.