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In an address 10 weeks since he declared a national state of disaster due to the coronavirus pandemic, Ramaphosa said "the risk of a massive increase in infection is now greater than it has been since the start of the outbreak in our country".
He said companies must develop a workplace plan before restarting, including implementing social distancing measures, screening and quarantining those infected.
Vulnerable staff including those over 60 or with chronic diseases should stay at home and be allowed to work from home if possible, he said.
"Subject to these measures, all manufacturing, mining, construction, financial services, professional and business services, information technology, communications, government services and media services, will commence full-time reopening from the 1st of June," he said.
Mining companies must comply with guidelines to prepare and implement a mandatory code of practice to mitigate and manage COVID-19 under new rules gazetted last week.
Mines, except collieries supplying power utility Eskom, had to close under "unprecedented" measures in the initial 21-day lockdown Ramaphosa announced in March.
Some companies then applied for exemptions and the government allowed mines to ramp up to a 50% workforce capacity in April as the lockdown was extended, with Impala Platinum charged for allegedly contravening the lockdown rules amid the confusion as the changes came into effect.
Industry lobby group, the Minerals Council South Africa, had warned in April an extended lockdown could put up to 45,000 jobs at risk.
Level four restrictions were put in place this month, allowing openpit operations to resume at full capacity and underground mines at 50%.
However some operations have since been suspended after outbreaks of COVID-19, including AngloGold Ashanti's Mponeng mine where 196 cases have been identified this week, and Impala Platinum's Marula where 19 cases were detected.
There are 263 confirmed COVID-19 cases in South Africa's mining industry and two deaths from the virus, according to the minerals council's figures yesterday.
There are 23,615 cases in the country and about 5.5 million globally, according to Johns Hopkins University today.