Queensland's state-owned utility Sunwater has been underpaying up to 400 staff for more than a decade, with the union saying it uncovered the bungle six months ago.

Key points: 130 current staff and up to 270 former staff underpaid

130 current staff and up to 270 former staff underpaid Changes during WorkChoices in 2006 could have led to contract confusion

Changes during WorkChoices in 2006 could have led to contract confusion Union raised issues six months ago, accused Sunwater of inaction

Sunwater has apologised over the error that began in 2006 and affected a quarter of its employees, largely technical specialists and senior leaders.

Professionals Australia union said it first suspected the issue six months ago during negotiations over a new enterprise agreement.

The union's Queensland director Adam Kerslake believed Sunwater had made an "honest mistake" but said they could have dealt with the situation better, and quicker.

He said they only acknowledged the issue late last week, when Energy Minister Dr Anthony Lynham intervened.

"The intervention from the Minister's office was so important, because they just went, 'this is wrong, you need to fix it', and Sunwater finally accepted responsibility for the extent of the problem," he said.

"Before that there were barriers.

"It was a complete bungle by the management.

"They should have been onto this early on and they should have responded early on when we first raised it with them, but they didn't.

"We were frustrated through the process."

Total backpay still being counted

Mr Kerslake said it was hard to estimate what the average worker would be owed, but they had investigated some members' situations in detail so far.

"Some people are entitled to tens of thousands in backpay, we think," he said.

"They've been working overtime and not being paid, etcetera etcetera.

"The staff are completely blown away, completely shocked."

The Services Union, who was also involved in the wage negotiations, said employees on individual contracts had been missing out on allowances they were entitled to under the collective enterprise agreement.

Secretary Neil Henderson believed the issue could have arose in 2006 because that is when WorkChoices came in.

Sunwater operates 19 dams to deliver about 40 per cent of the water used commercially in Queensland. ( Supplied: Sunwater )

He said at that time Sunwater's enterprise agreement switched over from state to federal jurisdiction, and became subject to different laws.

"Someone has made an assumption at some point that their individual agreements swept everything aside, and that was an incorrect assumption," he said.

"To work out what people are entitlement to, they will have to go back and identify what the employees were doing each week for the last several years.

"It's not an easy task.

"Anybody who has been employed at Sunwater in the past ... might be getting an unexpected Christmas bonus.

"They were in denial."

Sunwater chief executive Nicole Hollows, who announced last week she would be stepping down from the role, said 130 current staff are affected.

An external advisor would investigate how many past employees were affected and would calculate the entitlements owed.

"We expect that no more than 400 past and present employees have been affected," she said.

"This process is expected to take approximately six months to complete, however could potentially be extended.

"Sunwater was alerted to the potential application issue following the annual remuneration review in August 2019."