Around 38,000 Queensland Health workers will have to repay $62 million in over payments, as part of the state’s payroll debacle.

Queensland Health has revealed overpaid staff owe an average of $1100 each while one worker was overpaid by almost $100,000.

About 22,000 workers, overpaid up to $200, will not have to repay the funds, at a cost of $1.6 million.

The problem-plagued new pay system, introduced in March last year, resulted in staff being overpaid, underpaid or not paid at all.

Queensland Nurses Union assistant secretary Des Elder said the payroll system had been "a nightmare" for everyone involved.

Mr Elder said health workers were not obliged to pay anything back until they were satisfied with the accuracy of the overpayment allegations.

"There’s a fair bit of skepticism about the record keeping...that has been applied in the last 12 months or so," he said.

"We have tried to emphasise to Queensland Health that they do need to deal with some sensitivity in relation to how they approach people and they need to have processes in place where people don’t agree that they had been overpaid."

Mr Elder said the debacle had left employees reeling in the wake of the state’s devastating floods and cyclones and he said there were still glitches in the system.

"They are angry and they are still very upset their pays have been messed up to the extent that they have," he said.

"People are still exhausted from the natural disasters. This has taken its toll on people and this adds to that stress and anxiety and disillusionment that people are having with the whole system.

"It beggars belief really. I think there’s a lot of bridge building to be done."