When Nathaniel Garang produced a medical certificate after he had gastroenteritis, his boss at a health food factory said his time off work was "unacceptable" and would be taken out of his annual leave.

His manager threatened to never recommend him "as an honourable person/employee, due to your recent dishonest behaviour".

Fair Work Commission vice-president Adam Hatcher said Byron Bay Superfoods' conduct following its dismissal of Mr Garang "can only be characterised as vindictive".

It tried to prevent him getting Centrelink benefits after his job was terminated and questioned his GP's "ethics and medical due diligence" in a complaint to the Medical Board of NSW. The GP was accused of writing a medical certificate "based on a medically unfounded diagnosis".

Describing the experience as "really horrible", Mr Garang told Fairfax Media he was "really hurt by the terrible treatment".

His wife, Amy Garang-Hall, said the company's "disgusting" treatment of her husband had caused him sleepless nights.

"He was not only bullied and harassed by his supervisor and underpaid, they accused him of being dishonest when his GP said he had a gastro bug," she said.

"They sent letters to the Medical Board of NSW saying if he did have a gastro bug then why wasn't he quarantined from his wife who was heavily pregnant at the time."

The commission found Mr Garang was unfairly sacked from Byron Bay Superfoods in northern NSW in August last year after he complained about being underpaid and insisted on being paid according to the relevant modern award. It found Mr Garang should receive $10,694.84 in compensation.

Byron Bay Superfoods is a small food manufacturing business in Bangalow. The company, which touts itself as valuing "intuition over income and surfing over savings", makes snack foods including Wallaby Bites, Superfoodie breakfast slices, Le Granola Bar, Superbar, Forager and Jumbles.

The company employed Mr Garang in 2014 as a casual on $21 an hour and he became a full-time employee in March 2015 on an hourly rate of $22.01. Soon after being made full time, the Fair Work Commission heard evidence from Mr Garang that his supervisor began to bully him and referred to black people as "coloured people".

Born in South Sudan, Mr Garang lost his father and some of his siblings in a civil war when he was four.

He spent many years in a refugee camp in Kenya and arrived in Australia in 2005 on a humanitarian visa. He married in 2008, has three children and describes himself as "a proud Aussie", having become an Australian citizen in 2009.

Mr Garang was often required to work unpaid for 40 minutes a day and was forced to take a day off during quiet periods as annual leave.

After complaining to the Fair Work Ombudsman, he was offered $1000 to drop his complaint.

After his dismissal, Mr Garang had difficulty getting the Newstart allowance because the company refused to provide him with a separation certificate to confirm termination of his employment.

Describing him as "a witness of credit", Mr Hatcher said Mr Garang's evidence was "clear, consistent" and supported by documentation.

In contrast, the evidence of Byron Bay Superfoods managing director Paul Owies was "highly problematic" and "marked by inconsistencies and changes in position, and in important aspects was obfuscatory".

The commission found Mr Garang's dismissal was "harsh, unjust and unreasonable" and not a genuine redundancy.

Mr Owies told Fairfax Media that he was "very disappointed" with the commission's judgment and would appeal.

"This only hurts full-time employees in the future," Mr Owies said.

"We are not going to take on full-time employees. We'd prefer to have two casuals if we have to replace someone like that in the future."

Mr Owies said his company had fewer than 15 employees and had decided to make Mr Garang redundant because some of its products sold to Woolworths and Coles had been deleted.

"We are an entrepreneurial company and we are an innovator of world-class snack foods for the major retailers," Mr Owies said.

"It is a very competitive landscape in the Australasian region in the retail space and your product is only as good as it turns over on the shelf."