According to the latest figures from the Minerals Council South Africa, 1,739 of the 3,119 cases were from platinum mines, followed by 938 from the gold sector.
Platinum group metals mines had the biggest number of direct employees, about 164,500 of the mining industry's 455,000, in 2019.
About one in seven employees tested have returned a positive result, according to the figures.
The council said of the industry's 425,112 employees, 290,762 had been screened and 21,798 tests had been done.
The death toll has risen to 21 and 1,872 people have recovered.
However results were pending from 1,267 tests - with the council saying recently it was looking to add to the industry and country's testing capacity, given the "significant lag" in processing, the exigencies of mining operations and the high number of asymptomatic cases being identified.
The number of positive cases had reached the 1,000 mark mid-June.
Miners had to adopt mandatory COVID-19 guidelines in May after the Association of Mineworkers and Construction Union won a legal battle seeking binding regulations to protect workers.
However unions are pushing for universal testing for mineworkers.
The minerals council has denied the industry is the country's "epicentre" of COVID-19.
It said last week members were on a "myth-busting" mission to address stigmatisation surrounding the global pandemic, warning it could prompt risky behaviour including people denying they had symptoms.
It said yesterday the mining industry's test rate was 5.13%, higher than South Africa's 3.14% and the 3.3% global test rate.
In South Africa, the number of confirmed cases has risen to 215,855 and deaths to 3,502, according to Johns Hopkins University today.