The country's Water Ministry is urging an immediately program of building pumps and monitoring stations, the BBC reported Thursday.
Toxic acidic water has been building up in mine shafts dug underneath Johannesburg more than a century ago that stretch for many miles beneath the city.
The Department of Water Affairs has published a report by a panel of experts warning that if the water is allowed to continue to rise, it will start covering low-lying areas in the vicinity of the former mine at Gold Reef City, popular with tourists.
Water with high acid levels will affect property and infrastructure, the report says.
It recommends that intervention measures to drain acid mine water be made in the western, central and eastern basins of the city.
The South African government has said it would be feasible to have pumping stations in place by March 2012.
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