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The National Union of Metalworkers of South Africa said employers could not force workers to take paid leave during the lockdown, saying this had been confirmed by the labour department.
Labour minister Thulas Nxesi had told a media briefing on Tuesday: "Companies cannot force employees to take annual leave".
In an official statement, he confirmed the department was receiving concerns about workers being instructed to take paid leave and said it had issued a directive outlining the benefits employees would be entitled to under the Unemployment Insurance Fund.
"We do understand that in terms of the leave determination, employers can compel employees to take leave at any time as they deem fit," he said.
"However, this is a unique situation, that requires all of us to act in a manner that promotes social solidarity.
"We would like to express our sincere appreciation to the employers who have already demonstrated social responsibility and solidarity by not only paying workers in full during this lockdown, but also by making themselves available to assist us by acting as disbursing agents during this period."
NUMSA urged workers to contact their organiser or shop steward if they were unsure of their rights.
Resources minister Gwede Mantashe meanwhile conducted unannounced visits to three mines supplying coal to Eskom this week, to assess compliance with the lockdown regulations.
He said on Tuesday there were currently three confirmed cases of COVID-19 in the country's mining and energy sectors, one each in Gauteng, Mpumalanga and Western Cape.
South Africa had 27 new cases confirmed yesterday, taking its figures to 1,353 and five deaths, according to the World Health Organisation.