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Resources minister Gwede Mantashe said on Friday the mines department had received information about "incidents of non-adherence" at some mining houses.
"Our inspectors have been tasked to ensure compliance during this period and will intensify our visits both scheduled and unannounced to those mines still operating," he said.
"We are doing this not to be punitive, but with the primary objective of safeguarding the lives of employees, suppliers, contractors and all those they will come into contact with during this period."
Mantashe made surprise visits to three collieries last week - Exxaro's Matla, Glencore's Impunzi and Seriti's Kriel operations - which are among the companies continuing to supply coal to Eskom.
"We found that the mines are not at the same level in terms of their state of readiness to respond to COVID-19," he said.
"There are some pockets of excellence, while others are lagging behind."
He encouraged the mines to work together to share information and best practice.
He also commended the mining and energy sectors for offering support to assist the government in managing the spread of the virus.
"To date, about 770 beds have been made available for quarantine and self-isolation by a number of mining companies," he said.
AngloGold Ashanti (JSE: ANG) said last week it had worked closely with multidisciplinary teams from the provincial governments of the North West and Gauteng, to make available two hospitals for their exclusive use as part of the frontline COVID-19 effort.
The miner had also pledged R20 million (US$1 million) to the Solidarity Response Fund to assist the healthcare sector and provide humanitarian support.
Mantashe also noted some miners had applied for permission to keep operating, albeit at significantly reduced levels, in line with the Disaster Management Regulations' categorisation of essential goods and services which had been amended on Thursday.
He reiterated on Friday there were three cases of COVID-19 in the country's mining and energy sectors.
South Africa has 1,585 confirmed cases and nine deaths, according to the latest figures from the World Health Organisation.