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The Port Elizabeth Labour Court has declared the three month strike by Numsa members at the Port of Ngqura container terminal, as illegal.
The order applies to permanent Transnet employees who are to return to work on Wednesday for the first shift or they could face dismissal.
The court found that Numsa and its members had failed to follow procedures set out in the Labour Relations Act governing strikes.
The court also ordered Numsa to pay all Transnet's legal costs.
Transnet Group Chief Executive, Brian Molefe, told a media briefing on Tuesday that due to the strike, temporary employees have lost out on an opportunity to become permanent staff.
"A few members of the Numsa union who were on strike, needs to come back to work or face disciplinary action and possible dismissal. It applies to Transnet permanent employees only. One of the things that Numsa did was to take temporary employees on the strike at a period when we were just about to employ them on a full time basis, and unfortunately that opportunity has been lost to them" he said.