The owner of two Melbourne restaurants who paid his teenage employees with pizza and soft drink has been fined more than $330,000.

The Fair Work Ombudsman found 111 workers, mostly teenagers and some of them as young as 13, were underpaid a total of $258,000 over a three-year period at the Pakenham and Berwick outlets of La Porchetta.

In a judgement handed down in the Federal Circuit Court, Judge John O'Sullivan said the practice "belongs in the dark ages".

The court heard Ruby Chand, of Tecoma, who owned the franchises, claimed the employees were given half-price pizza and soft drink which was being offset against their wages and entitlements.

The workers were paid flat hourly rates which were below the minimum they were entitled to, trainees and apprentices were not paid the minimum number of hours they were employed to work and leave entitlements were underpaid.

Chand was fined $55,803 and his two companies which operate the restaurants were each fined $139,507.

The companies were also ordered to pay back more than $79,000 in outstanding entitlements.

Judge O'Sullivan said the nature and the extent of the breaches "warrants severe sanction by way of penalty".

"I am satisfied that the conduct engaged in by the respondents was part of a systematic business practice," he said.

In 2007, 2008 and 2009 the same companies were ordered to reimburse underpaid workers.