The operators of a cafe in Melbourne's inner north will face court after the Fair Work Ombudsman started legal action against the company, alleging they underpaid 73 workers more than $180,000.

Key points: The Fair Work Ombudsman alleges Barry cafe underpaid 73 employees at total of $180,660 over a 12-month period

The Fair Work Ombudsman alleges Barry cafe underpaid 73 employees at total of $180,660 over a 12-month period The owners of the Northcote cafe will face the Federal Circuit Court on October 16

The owners of the Northcote cafe will face the Federal Circuit Court on October 16 Individual workers were allegedly underpaid between $31 and $12,315 each

The owners of Northcote's Barry cafe, siblings Stavros and Anastasia Petroulias, and the company they part-own and operate Malevi Pty Ltd will face a directions hearing in the Federal Circuit Court on October 16.

This follows an ABC investigation last year, when former staff accused the cafe of underpayment by at least $5 an hour.

The Fair Work Ombudsman (FWO) alleges that Barry employees were paid flat rates of between $18 and $23 an hour, resulting in underpayment of ordinary hourly rates, casual loadings, overtime rates and penalty rates for weekend and public holiday work, which they were entitled to under the Restaurant Industry Award.

Under the award, the minimum hourly rate should have been $24.41 for weekday shifts, and $29.30 for weekends.

The FWO alleges that 73 employees were underpaid a total of $180,660 over between April 2017 and April 2018.

Alleged underpayments of individual workers ranged from $31 to $12,315, the FWO says.

The FWO also alleges that Malevi Pty Ltd, Mr Petroulias and Ms Petroulias unlawfully took adverse action against one employee by not allocating further shifts to him because he exercised a workplace right by asking about wages he was owed.

This employee's pay rate was less than he was entitled to under the award, the FWO alleges, and the employee indicated he would initiate small claims proceedings to recover unpaid wages.

The FWO is also alleging breaches of record-keeping laws.

Former staff and members of United Voice staged a protest at Barry cafe last year. ( ABC News: Jessica Longbottom )

Fair Work Ombudsman Sandra Parker said inspectors discovered the alleged underpayments when they investigated reports of workers being underpaid at the cafe.

"Enforcing compliance with workplace laws in the fast food, restaurant and cafe sector continues to be a priority for the Fair Work Ombudsman," Ms Parker said in a statement.

"Employers in this sector are on notice that they must pay all employees according to Australia's lawful minimum pay rates.

"We also treat very seriously allegations of employers taking any sort of action against an employee in response to an employee simply seeking to have their lawful workplace rights respected."

The FWO is seeking court orders requiring Mr Petroulias, Ms Petroulias and Malevi Pty Ltd to backpay the employees in full.

Mr Petroulias and Ms Petroulias each face penalties of up to $12,600 for each contravention and the company up to $63,000 for each contravention.

The FWO is also seeking court orders requiring the company to commission an independent audit of its wage payment practices and provide the results to the FWO, display a workplace notice detailing workers' rights and obtain workplace training.

The ABC has attempted to contact the cafe owners for comment.