In a statement of agreed facts tendered to the Federal Circuit Court, Westside Petroleum Retail and three of its management staff underpaid 22 employees at 12 regional stations a total of $62,393 between 2015 and 2016.

The company has been penalised $45,000 and general manager Patrick Riad, company accountant Francesco Ieraci and area manager Shahzaib Khawaja have each been penalised $4000.

The company paid employees unlawfully low, flat rates between $15 and $25 an hour that led to underpayment of employees' casual weekday, weekend, public holiday and overtime rates under the relevant award.

The 22 affected workers were underpaid amounts ranging from $347 to $7772, with four of them aged just 19 years old at the time. Two were visa holders and one was on a 489 regional sponsored visa.

The average underpayment was $2836 each, while three were underpaid nearly $6800.

All employees have been back paid in full and no allegations have been made against any franchisee-run stations.

The agreed court document states Mr Khawaja was responsible for negotiating, setting and communicating the low, flat pay rates with no additional amounts for penalties or overtime.

This included not sending negotiated pay rates for new employees to the accounts team.

The court document also states that Mr Riad and Mr Ieraci were aware of the underpayments.

The Westside Petroleum-operated stations in the Riverina are Docker Street, Wagga; Bourke Street, Tolland; and Hoskins Street, Temora.

Judge Robert Cameron found that the underpayments were deliberate and said they were "not insignificant", with some employees underpaid about $1000 per month.

Westside Petroleum had argued that it was rapidly expanding at the time, but Judge Cameron said "the commercial imperative to seize new business opportunities can explain distraction from issues of compliance but it does not excuse it".

"It is unacceptable that Westside Petroleum focused on the growth of its business and failed to have proper regard to very basic employer obligations," Judge Cameron said.

He ordered the company to provide its franchisees with information about workplace laws and display workplace notices providing information on workplace laws.

Rostron Carlyle Rojas, the law firm representing Westside Petroleum, said in a statement on behalf of the company that the findings and penalty were accepted.

"The underpayments have been rectified and processes have been put in place so this mistake does not happen again," the statement reads.

"Westside Petroleum apologises to all staff that were affected by this."

Fair Work Ombudsman Sandra Parker said the matter serves as a warning to employers about paying flat rates rather than applying the relevant award.

"The Fair Work Ombudsman has been highlighting for many years that the use of low, flat rates that undercut lawful minimums is a clear breach of workplace laws," Ms Parker said.

"Any employer paying their staff with flat rates less than the relevant minimum rate faces enforcement action.

"Any employees with concerns about their pay should contact us."

Parker started court proceedings against the company and its three management staff in March after requests for help from employees led to inspectors auditing the company.

Of the more than 50 service stations in the Westside Petroleum network, there are 47 in NSW.

Prior to Wagga's Westside Petroleum-branded station opening in August 2018, the site was a Shell-branded station.

It re-opened after 10 months of renovations.

According to the Fair Work Ombudsman, the other nine stations where workers were underpaid were Adaminaby, Finley, Gurley, Lismore, Somerton, Blayney, Glen Innes, Peak Hill and Cooma.