Fracking is a threat to water resources in the greater Karoo, the Wildlife and Environment Society of SA (Wessa) said on Thursday.
"Any pollution or degradation, particularly in the Karoo, including areas of global biodiversity hotspot status, could cause disastrous ecological, social and economic consequences," Wessa conservation director Garth Barnes said in a statement.
While Wessa understood the potential economic benefits of fracking, it believed the government was not taking the full spectrum of sustainable development into consideration, he said.
On Monday, Water and Environmental Affairs Minister Edna Molewa said a notice of intention to declare fracking a controlled activity had been gazetted.
"What this means is that fracking becomes a water use, thus requiring a water use licence," she said.
The notice, in terms of the National Water Act, was gazetted on August 23, and allowed 60 days for public comment.
Fracking, or hydraulic fracturing, is the process of fracturing rock by a pressurised liquid to extract natural gas from shale rock layers deep within the earth.
When considering licences, Molewa said only issues around water resources, such as the potential impact of chemicals used in the process, would be considered.
Barnes urged the government to exercise the precautionary principle enshrined in the National Environmental Management Act.
"The act obligates the proponents of an activity to provide proof that it will not cause harm to the natural environment or people before the activity is allowed to go head," he said.