Mines countrywide have been filling with water, creating a toxic sludge that leaches into ground water or decants into rivers. Millions have been spent on mitigation as the state struggles to keep the problem in abandoned mines below the critical level.
As the state battles to at least neutralise acid mine drainage, if not purify it, there are concerns about deteriorating water quality in the Vaal River system and its effect on rural communities and agriculture.
Department of Mineral Resources chief financial officer Irene Singo said the best estimate of closure costs was R45.1bn, of which R44bn was for class A mines - gold, coal, lead, copper, platinum, silver, uranium and nickel - posing a high environmental threat. Class B and C mines, which pose lesser dangers, would cost R1bn.
The cost of rehabilitating asbestos mines was R2bn, of which R200m was disclosed as a provision while R1.8bn was disclosed as a contingent liability, she said.
The contingent liability is in all likelihood to cover potential lawsuits against the state from individuals suffering from asbestosis.
To date, emergency work to contain acid mine drainage has cost R2.6bn while maintaining this until 2018 is estimated to need R875m.
Ms Singo said a key risk on the Witwatersrand was water security as well as water quality and socio-economic development.
But Tracey Davies, a lawyer at the Centre for Environmental Rights, said: "We face a massive regulatory failure as neither department (water affairs and sanitation nor mineral resources) requires a levy from mining companies to treat water and there is no enforcement of the laws."
There are estimated to be 6,000 derelict and ownerless mines across SA. The department' presentation showed that 245 of these were old asbestos sites.
"Given the health and environmental concerns, the rehabilitation of former asbestos mining areas was the highest priority; followed by the sites proximal to communities, with the greatest risk to the health, safety and environment," the presentation read.
SA ceased asbestos mining in 2003 and banned it in 2008.
Ms Singo noted that asbestosis was an incurable chronic disease.
"Communities affected by asbestos mining started to sue the government. As a consequence, the government made a commitment to initiate "asbestos rehabilitation," she said.