The health department is auditing potential underpayments made to day-shift workers after it found two lots of overpayments totalling $291,000 to 3700 hospital and health service staff over eight years.
Health Minister Yvette D'Ath says some workers were overpaid by up to $100 but most received only about $1 more than they were entitled to, so the government won't make them pay back the funds.
She says the department is now auditing the $16 billion payroll to work out how many workers were underpaid and the total amount, which is likely to be more than the $291,000 in overpayments.
"It is not, I guess, out of the realm to assume that, you know, it could be in the millions," Ms D'Ath told reporters in Redcliffe on Friday.
"But we just don't know the exact figure yet, but this is, as I say, money owed to individuals.
"They're likely to be, you know, quite small amounts, but lots of individuals, but I want to get the proper data so I can be accurate."
Hospital and health services will need to cross-check their records, but the department intends to pay affected staff in batches of 50 rather than waiting for the full cohort to be confirmed, to speed up the process, which may not be finalised until June 30.
"Of course, that's not an extra cost to taxpayers," Ms D'Ath said.
"This is just what workers are entitled to, and they will be paid that amount of money."
The minister brushed off questions about whether the payroll system was fit for purpose, saying an external audit found it to be compliant with the state's workplace awards and enterprise bargaining agreements.
Ms D'Ath stressed that with almost 120,000 shift workers on the health roster there were millions of dollars in underpayments and overpayments every year "as a matter of course".
She said that's because a worker's shift will often change during a pay cycle due to overtime, shift swaps or workers being sick.
"And so those things happen. As a matter of course, when you've got 1000s of 1000s of shift workers and their shifts changing quite often, especially when we saw, you know, lots of people not being able to work because of COVID and lots of people actually working longer hours because of COVID."
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