Statistics South Africa said the data, released late last week, showed the COVID-19 pandemic and lockdown regulations had "an extensive impact on economic activity".
The department said PGM production fell 62% compared with a year earlier, iron ore fell 68.7%, gold 59.6% and manganese ore by 57.6%.
It said seasonally adjusted mining production decreased by 34.1% in April compared with March 2020.
Collieries supplying Eskom had been allowed to continue operating during the shutdown, then some companies applied for exemptions, with restarts causing confusion and prompting a union to seek binding regulations to protect mineworkers from the pandemic.
Openpit operations were then allowed to resume at 100% workforce capacity and underground at 50% in May and the industry was allowed to return to full capacity this month as measures to prevent the spread of COVID-19 eased.
However Harmony Gold CEO Peter Steenkamp had said in late May it would probably take the company, which has one openpit and nine underground mines in South Africa, about a month to return to full production.
The Minerals Council South Africa had estimated the country's mining production would be impacted up to 10% this year due to the global COVID-19 pandemic.
The council indicated last week about 240,000 miners were back at work.
The industry employed about 455,000 people in 2019.
There has been one death and 879 positive cases of COVID-19 in the country's mining industry, from 255,744 screened and 10,478 tested, according to the council's latest figures on Friday.