Queensland Health payroll problems have seen staff overpaid by nearly $110 million in recent years.

New figures suggest the pay bungle, which has been ongoing since 2015, has left a quarter of the state's public health workers with an outstanding debt.

Compounding the waste, Queensland Health has been paying for debt collectors to recoup some of the money.

Since FY2015-2016, $109,152,293 has been incorrectly paid to departmental staff, according to figures obtained by the ABC.

There are currently about 40,000 current or former Queensland Health workers being pursued to repay around $29 million in inflated wages.

“Each fortnight, on average, more than 118,000 pays are processed, and more than $240 million net is paid to staff across Queensland… overpayments account for less than 0.3 per cent of the fortnightly net pay run,” a spokesperson told reporters.

“The majority of overpayments are the result of the late submission of forms where retrospective adjustments were made for rostered shifts that were paid but not worked due to unplanned leave or other circumstances.”

An earlier payroll debacle in 2010 saw Queensland Health underpaid, overpaid, or not paid at all, costing taxpayers $1.2 billion.

Some of the current debts are linked to the issues experienced in 2010.