The former owner of a Melbourne fruit shop has been handed a record fine for underpaying an Afghan refugee who went weeks without wages.

Fair Work Australia fined Abdulrahman Taleb, the former owner and operator of Sunshine Fruit Market in Sunshine, about $16,000 and his company $644,000 for deliberately ignoring warnings about pay rates and withholding pay.

The Federal Circuit Court found the worker, who was a refugee from Afghanistan and spoke little English, was paid nothing for a number of weeks in 2012.

He was later paid a flat rate of $10 per hour to the maximum of $120 a day for stacking and moving fruit and vegetables.

He should have received a normal rate of $17 per hour and $38 on weekends and $43 on public holidays.

Fair Work Australia said the worker was underpaid a total of $25,588 for two separate periods in 2012 and 2013.

He was also not provided with the required meal breaks, despite sometimes working more than 12 hours a day.

The punishment was a record for the Fair Work Ombudsman, overtaking a fine handed out in February to a former owner-operator of a cafe in Albury.

Judge Philip Burchardt said Taleb's underpayments were "egregious".

"The underpayments were so significant that the total not paid to [the worker] was, in relative terms, enormous for such a short time," he said.

"I accept the submission of the [ombudsman] that the way it worked out was that [the worker] was paid wages of between $3.49 and $9.29 per hour."

Afghan refugee 'vulnerable', judge says

Judge Burchardt said the business was not lawfully run, with all wages made in cash and the company in breach of a number of workplace regulations.

The worker had come to Australia as an asylum seeker and spent time in detention before being released and granted residency in 2010.

"[The worker] was a vulnerable employee in that he was a recent arrival to Australia and totally lacked fluency in English, and could reasonably be understood to be most unlikely to be aware of any entitlements at law," Judge Burchardt said.

The judge said Taleb, from Altona North, had never apologised and his contrition was "unimpressive".

Fair Work Ombudsman Natalie James said 18 per cent of people who approached Fair Work about issues with their employers were either migrants or on a visa, but they only made up 5 per cent of the overall workforce.

"Visa workers and migrant workers are very vulnerable for a range of reasons and in this case, the worker had very little fluency in English and we were able to use translators to work with him," she said.

She said the case served as a warning to employers that they would be prosecuted for flouting the law.

"I think this is an example of ruthless exploitation on the part of this employer, this is an individual who the court described as uncooperative and aggressive under cross-examination, and also described him as an overbearing and unimpressive witness," she said.