The Ombudsman has filed a Federal Court action against the Hero Sushi chain for underpayment at three stores in Canberra, Newcastle and the Gold Coast.

It is alleged the operators failed to pay minimum hourly rates, casual loadings, penalty rates, overtime, clothing allowances, annual leave entitlements and superannuation, or provide payslips.

The operators are also accused of creating false records to provide to Fair Work inspectors during their investigation, showing inaccurate hours of work or claiming employees had been paid higher rates and superannuation when they had not.

Forty-three of the 94 affected workers are from the Canberra Centre Hero Sushi.

Court documents show some Canberra employees were paid flat rates between $12 and $16 an hour.

They reveal that rosters and payslips were falsified to make out workers were paid more and worked fewer hours.

One Canberra employee was said to have been paid $2667 for 103 hours from February 8-21 in 2016, with $867 of tax remitted and $253.37 paid in superannuation.

In fact the staff member worked 114 hours over the fortnight and was paid $1572.47. No tax or super was paid either.

Annual and personal leave was also not accrued for staff, although the fake records suggested it was, and hourly rates were also inflated.

Fair Work Ombudsman Sandra Parker said many of the workers were young Korean and Japanese nationals on international student and working holiday visas.

She said the sheer number of staff who had allegedly been underpaid was "alarming and very serious conduct".

“The Fair Work Ombudsman considers all allegations of worker exploitation seriously, particularly matters involving migrant workers who may have little understanding of their workplace rights or how to seek help," Ms Parker said.

"All workers in Australia have the same rights at work, regardless of citizenship or visa status."

The underpayments were uncovered during a blitz of sushi businesses during 2016.

It is alleged workers across the three outlets were underpaid $694,628 between April 2015 and July 2016.

The Ombudsman is seeking a court order requiring all outstanding backpayments and superannuation to be paid.

The matter is listed for a directions heading in the Federal Court in Sydney on March 12.

The three corporations named in the action - HSCC Pty Ltd, HSCK Pty Ltd and HSPF Pty Ltd - could face penalties of up to $54,000 per breach.

Company directors Deuk Hee “William” Lee and Hokun “Robert” Hwang could also face penalties of up to $10,800 per contravention.

Payroll officers employed at Hero Sushi's head office in Chatswood, Chang Seok “Tommy” Lee, Ji Won “Brian” Cho and Jung Sun “Jimmy” Kim, are also named as respondents in the suit.

The action comes amidst an increased focus from the Ombudsman on sushi store operators.

The workplace watchdog audited 45 sushi stores across the ACT, NSW and Queensland after an increase in calls for help from staff last year, Ms Parker said at the time.

While only a fraction of stores audited were targeted due to allegations of underpayment, Fair Work inspectors found 39 broke workplace laws. Of the seven Canberra businesses audited, five were deemed to have breached at least one workplace law.

"Although everybody loves cheap sushi, perhaps we should ask ourselves - is what I’m paying enough to cover workers’ minimum wages and entitlements?” Ms Parker said last year.

Ms Parker urged migrant workers concerned about their pay to contact the Ombudsman, regardless of their visa status.

"We have an agreement with the Department of Home Affairs where visa holders can ask for our help without fear of their visa being cancelled," Ms Parker said.

For help, visit fairwork.gov.au or call the Fair Work Infoline on 13 13 94.