Edison Peng and his company JMSL Pty Ltd, which owns and operates the Coffee Club outlet at the Westfield Geelong shopping centre, allegedly paid two junior workers a flat rate of $15 an hour between 2016 to 2018, totalling $15,412 in underpayments.

One worker, aged 19 to 20, missed out on $12,910 of pay between May 2016 to August 2017, a statement from Fair Work on Tuesday claims.

The second worker, 20, was underpaid $2502 over a three-month period in 2018, before the pair contacted the ombudsman for help.

"The alleged payment of low, flat rates that undercut award entitlements is completely unacceptable conduct and we treat underpayment of young workers particularly seriously," Ombudsman Sandra Parker said in a statement.

It's also alleged Mr Peng and his company provided "false and misleading" records and payslips to Fair Work inspectors investigating the matter.

"Employers should be aware that the Fair Work Ombudsman takes allegations of false and misleading records extremely seriously," Ms Parker said.

While most of the alleged underpayment has been repaid, the ombudsman is seeking a court order to make Mr Peng and his company cough up the rest.

It also wants Mr Peng to complete workplace relations training.

A directions hearing has been set for November 12 in the Federal Circuit Court.

Australian Associated Press