The Fair Work Ombudsman secured the penalties against Westside Petroleum and three of its management staff for underpaying the 22 employees.

The underpayments took place at 12 NSW and Victoria petrol stations between July 2015 and May 2016.

Inspectors audited Westside Petroleum after requests for help from employees.

In the Federal Circuit Court, Westside Petroleum Retail 1 was penalised $45,000.

General manager Patrick Riad, company accountant Francesco Ieraci and area manager Shahzaib Khawaja were each penalised $4000.

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Ombudmsan Sandra Parker said Westside Petroleum had been paying the employees unlawfully low flat rates from $15 to $25 an hour.

This led to underpayment of their casual weekday, weekend, public holiday and overtime rates under the Vehicle Manufacturing, Repair, Services and Retail Award.

"[We have] 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."

The 22 workers, the youngest of whom were aged 19, were underpaid amounts from $347 to $7772.

They have all been back-paid in full.

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

Westside Petroleum submitted 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," he said.

He ordered the company to give its franchisees information about workplace laws and to display such information.