Two juice shops, located in Werribee and Geelong, are facing allegations they underpaid staff wages.

The Fair Work Ombudsman has commenced legal action against the operators of two Hello Juice outlets, alleging they underpaid 27 workers a combined total of $38,458 across several months of 2017.

The Ombudsman is taking Skypac Group Pty Ltd and Skypic Group Pty Ltd, which operate Hello Juice outlets in shopping centres at Werribee and Geelong, to the Federal Circuit Court.

Legal action is also being taken against Victorian woman Hua Gong, who was the general manager of both stores.

The Ombudsman has alleged that some Hello Juice employees were paid flat rates as low as $10 per hour, which resulted in underpayment of the ordinary hourly rates, casual loadings and penalty rates for weekend and public holiday work they were entitled to.

Workers at the Geelong store were allegedly underpaid $23,902.47 and workers at the Werribee store were allegedly underpaid $14,555.64 in total.

Ms Gong and Skypac Group Pty Ltd also allegedly breached laws relating to cash-back arrangements on two occasions, by requiring a worker at the Werribee store to pay amounts totalling $1300 to cover part of a rectification payment and a tax refund payment made to her.

The Ombudsman said that Ms Gong and Skypac Group allegedly breached workplace laws by providing its inspectors with false or misleading records, and allegedly breached laws relating to pay slips and record-keeping.

The Ombudsman is seeking court orders requiring the companies and Ms Gong to back-pay the Hello Juice employees.

Fair Work Ombudsman Sandra Parker said inspectors discovered the alleged underpayments during self-initiated audits.

A directions hearing for the matter has been listed in the Federal Circuit Court in Melbourne for November 15.