The Daily Voice reported that Capewell Springs factory workers in Epping felt the time limit was unreasonable.
"This is a violation of our human rights...[Two weeks ago] money was deducted from my wages for time lost," 40-year-old Keith Hector said.
A photo of one of his payslips showed a deduction of R40, with "LOST" listed under the description.
Shop steward Dulon Beneke, 39, said he had to take time off when he got a stomach bug.
"I had to take sick leave because I can't afford to run to the toilet every time."
A labour department official told the newspaper the Basic Conditions of Employment did not go into detail about toilet breaks, but expected common sense to be applied.
Capewell Springs director Graham Montgomery refused to speak to the newspaper.
"I have nothing to say to you," he said before ending the call.
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