Aged care receptionist Jennifer Kimber was sacked from a NSW south coast nursing home in July last year after refusing to have a flu jab.

The Fair Work Commission refused her permission to appeal on Monday after ruling against her unfair dismissal claim in May.

Fair Work deputy president Lyndall Dean said the decision was a serious injustice to Ms Kimber which denied her protections under workplace law.

"Never have I more strenuously disagreed with an outcome in an unfair dismissal application," Ms Dean said.

Vice president Adam Hatcher and commissioner Bernie Riordan said they would not give any encouragement to a spurious objection to a lawful workplace vaccination requirement.

In a majority decision, they said Ms Kimber held broader anti-vaccination views and had told the commission her research about the flu jab was based on a Google search of "all sorts of stuff".

Ms Dean said it was highly inappropriate to label the sacked worker an anti-vaxxer.

She declared mandatory immunisation could not be justified in "almost every workplace in Australia".

"All Australians should vigorously oppose the introduction of a system of medical apartheid and segregation in Australia," she said.

"It is an abhorrent concept and is morally and ethically wrong, and the anthesis of our democratic way of life and everything we value."

Ms Dean said she would have granted the appeal, quashed the decision and had Ms Kimber reinstated to her old job.

Ms Kimber unsuccessfully argued she should be exempt because she suffered a rash after receiving a flu shot in 2016.

The majority decision found she provided little evidence of the condition and didn't tell management.

A manager was aware colleagues were told she was seeing a naturopath and trialling alternative treatments.

Sapphire Coast Community Aged Care took no issue with her refusal in 2017, 2018 and 2019, but sacked her in 2020 after the coronavirus pandemic started.

Ms Dean argued all COVID vaccines remained part of a clinical trial because they had provisional approval from the Therapeutic Goods Administration.

"This is not part of a conspiracy theory. It is a fact easily verifiable from the website of the TGA."

She said the requirement for consent in clinical trials should not be controversial, referencing the Nuremberg Code formulated in response to Nazi doctors' experiments.

"Coercion is completely incompatible with consent," the commission deputy president said.

"Denying a person the ability to work and participate in society if the person does not have a COVID vaccine will unquestionably breach this fundamental and internationally recognised human right."

Ms Dean said the "cure" was no longer proportionate to the coronavirus risk, warning governments and employers against hysteria and fear-mongering.

She said research showed many vaccine-hesitant people were well educated with legitimate concerns which were better addressed through education.

"Blanket rules, such as mandating vaccinations for everyone across a whole profession or industry regardless of the actual risk, fail the tests of proportionality, necessity and reasonableness."

Ms Dean was appointed to the commission by the coalition government in 2016.

Australian Associated Press