The payroll glitch ailing Queensland Health may be affecting all other state government departments, the Industrial Relations Commission has heard.

Tens of thousands of health workers have been underpaid, overpaid or not paid at all due to problems in new pay software that came online 12 weeks ago.

The IRC heard last night the difficulties are continuing, because the glitch in the health department's computer system appears to exist across all government departments.

"They told us that they couldn't turn off that function in the computer payroll system, because it was a whole-of-government configuration," Queensland Nurses Union secretary Gay Hawksworth said.

Comment has been sought from Queensland Health.

It is understood 180,000 people are employed across all state government departments.

Ms Hawksworth said nurses were told yesterday the incorrect payments could only be adjusted manually.

"Of course that's open to significantly more errors because there's 74,000 people on that payroll," she said.

"One would think you would also have to know what you're looking for. It would seem impossible for them to find and manually adjust every employee who has been overpaid."

It is understood up to 2000 manual adjustments need to be made each pay cycle.

Ms Hawksworth said the automatic deductions breached its enterprise bargaining agreement.

"It's certainly deducting money that are not overpayments. They are in fact deducting people's own money again," Ms Hawksworth said.

"Suddenly some people are being left again with no pay, or substantially less pay, again."

Queensland Health has until 4pm today to explain to the union what it has defined as a "financial disadvantage" to employers under the ongoing payroll problems.

It has until next week to produce a list of all payments made to each employee since the rollout of the new pay system in March.

Queensland Health director-general Mick Reid admitted the unauthorised deductions were illegal.

"It is against the enterprise bargaining agreement we have with the union and that's why we are rapidly trying to rectify the problem," Mr Reid told ABC Radio.

Queensland Health also has to detail how workers' group certificates will be affected.

The two parties will meet again next Wednesday before facing the Industrial Relations Commission again on Thursday.

"We need some IT programming expertise to explain to us why it's happening, what the configuration is, and then why they cannot turn that off," Ms Hawksworth said.

"We do not know if this system is fixable."

Although she said it was not clear for how long the problems would persist.

"They certainly did not provide me with any comfort that they had any clear idea of when this matter will end."