The decision by 7-Eleven to dismiss an independent wage panel set up to investigate the underpayment of its workers has been questioned by the Fair Work Ombudsman and Opposition Leader Bill Shorten, who labelled the move "disturbing".

The panel headed by Professor Allan Fels will end its work on Friday after the convenience store operator announced it was replacing it with an internal unit.

Professor Fels told the ABC's 7:30 program the move was unacceptable and accused the company of trying to minimise the payout to affected workers.

But the company's chief executive Angus McKay dismissed the claim, saying the panel was not doing enough to weed out invalid claims.

"We wanted to work with the panel to increase the level of scrutiny. We couldn't get to a place where the panel would agree to what we believed was the right process and right level of diligence," Mr McKay said.

"Given we couldn't come to terms, we now need to do it internally.

"We have every intention of processing every claim. My one caveat on that is we're only going to pay valid claims."

7-Eleven chairman Michael Smith also defended the company’s decision, telling 7.30 on Thursday that: "I really don't think we can outsource our morality".

"This is a case of taking it fairly on ourselves to make it right," he said.

In a statement, Fair Work Ombudsman Natalie James said she "noted with concern" the dismissal of the panel.

She said the regulator still had active investigations into a number of franchisees.

"There is also a real prospect that we will take legal action against more 7-Eleven operators," Ms James said.

"We are yet to be satisfied that 7-Eleven is meeting the expectations we have of it following the public release of our findings [from a recent inquiry into the company]."

Shorten 'disturbed' by dismissal of 7-Eleven wage panel

Opposition Leader Bill Shorten said the removal of the panel was "a new and disturbing twist" to the saga, which he labelled "exploitation on an industrial scale".

"[Professor Fels] has been sacked," he said.

"I understand now that the company's decided they will just check these matters out themselves.

"I also understand they're going to set a higher standard for evidence than the reasonable standard which Professor Fels and other independent people were using.

"We hear reports about threats to the 7-Eleven workers making claims. I am deeply disturbed at this turn of events."

He criticised the Federal Government for not acting in the wake of an Senate inquiry into the underpayments.

Panel ensured workers' confidentiality, union says

The wage panel was established after the ABC's Four Corners uncovered evidence that some workers were being paid as little as $10 per hour.

The union for retail workers also criticised the move to dump the panel, saying workers were concerned about their claims being handled by the company that "cheated" them out of millions of dollars.

"That was one of the key planks of the independent panel, was its capacity to keep claims confidential," Gerard Dwyer from the Shop, Distributive and Allied Employees Association said.

"But there were experts on that panel that also ensured that a claim had to stack up. Fair, transparent and confidential."

7-Eleven 'must accept moral and ethical responsibility'

Ms James moved to allay fears among some employees, particularly those on working visas, about coming forward to make claims now the panel was gone.

"They have our assurance that if they assist us with our inquiries into wage theft we will request that their visa status will not be prejudiced," she said.

Professor Allan Fels said he did not agree to the panel's dismissal. ( AAP: Alan Porritt )

She said 7-Eleven had to "accept it has moral and ethical responsibility" all workers were paid their entitlements and to comply with workplace laws.

Professor Fels rejected 7-Eleven's position that the removal of the panel was agreed upon by both parties, and insisted the panel was sacked.

"I sat there and listened in silence. I didn't agree to that and I don't agree with what they're doing," he told 7:30.

Mr Mckay dismissed the idea there had been "tension" between the panel and the company's management.

"We've been asking the panel lots of questions. But I think tension overstates it. We want more people to be paid … and we want to make sure there is no risk that people who should not be paid get through the system."