The supermarket giant on Tuesday said it learned it had underpaid 5700 salaried staff over nine years when a handful of store managers complained they were earning less than their staff.

It says it will return the cash, at an average of around $50,000 per staff member, plus interest.

Interim back payments will be made before Christmas, with the majority of affected staff being current and former department managers at store level.

None of the 145,000 staff covered by an enterprise agreement were affected.

Group chief executive Brad Banducci said Woolworths also expects to make a contrition payment.

"As a business we pride ourselves on putting our team first, and in this case we have let them down," Mr Banducci said in a statement.

"We unreservedly apologise.

"The highest priority for Woolworths Group right now is to address this issue, and to ensure that it doesn't happen again."

Mr Banducci said he expected to forfeit his bonuses but would not be drawn on his future.

The Fair Work Ombudsman will conduct an investigation and has vowed to hold Woolworths to account for breaching Australia's workplace laws on a massive scale.

Ombudsman Sandra Parker says she's shocked Woolworths has joined other big companies including Wesfarmers, Qantas, Commonwealth Bank, Super Retail Group and Michael Hill Jewellers in underpaying staff.

Sunglass Hut, 7-Eleven and George Calombaris' hospitality group MAdE are others to admit wage underpayment recently, while accusations have also been levelled at Neil Perry's high-end Rockpool restaurant chain.

The underpayment was uncovered by Woolworths in a review triggered by the implementation of the new enterprise agreement covering its supermarkets and Metro stores.

Woolies said it has only analysed two years of data but the issue could date back to 2010.

More underpaid staff could be uncovered when the company extends its review to all its Australian businesses, which include Big W department stores and Dan Murphys and BWS liquor.

"Lately, we are seeing a disturbing number of large corporates publicly admitting that they have underpaid their staff," Ms Parker said in a statement.

"Some of these matters go back many years and several comprise millions of dollars owed to workers. This is simply not good enough."

The retail union, the SDA, says it will be in stores talking to impacted salaried workers to ensure they are supported as needed.

It has called on all retailers to audit their payroll settings especially for salary staff.

Federal Labor's industrial relations spokesman Tony Burke says they have been calling in vain for five years for the Liberals to do something about worker underpayment.

Mr Burke said Prime Minister Scott Morrison does not take wage compliance seriously and that sent a message to businesses that they don't need to take it seriously either.

Labor wants a wide-ranging parliamentary inquiry into the issue, he said.

Australian Associated Press