Abdulrahman Taleb, former operator of Sunshine Fruit Market, was found to have paid the Afghan refugee as little as $3.50 an hour.

"For some of the time Mr Kazemi was simply not paid at all," Judge Philip Burchardt said in his judgment, describing the underpayment as "enormous" and "egregious".

Syed Jamal Udin Kazemi, understood to be in his 20s, was initially unpaid and later received a flat rate of $10 an hour up to $120 a day for his work at the market, the court found.

He should have been paid hourly rates of about $17 on weekdays, up to $35 on weekends and up to $43 on public holidays under the relevant award.

"The underpayments were so significant that the total not paid to Mr Kazemi was, in relative terms, enormous for such a short time," Judge Burchardt found.

"This was not a properly and lawfully run business. It was conducted in plain breach of a number of workplace regulations."

The now-deregistered company, Mhoney Pty Ltd, was fined $644,000, while Mr Taleb was personally ordered to pay $16,020 – in total the largest-ever penalty awarded in a Fair Work Ombudsman litigation.

His lawyer Fatoum Souki noted the size of the penalty and indicated Mr Taleb was not in a position to appeal the decision, but made no further comment.

Fair Work Ombudsman Natalie James said the case highlighted the vulnerability of workers who spoke little English and were on visas.

Of all requests for assistance from the ombudsman in 2016/17, 18 per cent came from workers on visas – an increase on the previous year and significantly disproportionate to the total number of workers on visas.

Half the cases that made it to court involved a visa worker, Ms James told Fairfax Media.

"It is pretty outrageous and it's sad we are still seeing examples of vulnerable visa holders being exploited in this way," she said.

Mr Kazemi approached the ombudsman after the conclusion of his second period of work, in January 2013, suspecting he had been underpaid.

But Ms James noted "for a lot of workers it's very hard to come forward, particularly where they don't have very strong English language skills".

In his judgment, Judge Burchardt said he believed Mr Taleb "took advantage" of Mr Kazemi's vulnerability.

He described Mr Taleb as a significant figure in Melbourne's Lebanese Muslim community, but condemned him as an "unimpressive" witness who had shown no contrition and had not apologised to his employee.

Mr Kazemi came to Australia as an asylum seeker and spent time in immigration detention before being granted residency in late 2010, according to the Ombudsman.

Fair Work offers a mobile application, Record My Hours, enabling workers to log their hours of work and pay slips in 18 languages.

The Sunshine Fruit Market is no longer owned or run by Mr Taleb.