Water and Environment Affairs Minister Edna Molewa has angered activists by allowing an Australian company to resume mining on the doorstep of the Mapungubwe World Heritage site.
The Save Mapungubwe Campaign, a coalition of seven groups, said the minister's decision was "contrary to the ordinary procedure stipulated in the National Water Act."
The mining licence, granted to UK-listed Coal of Africa in March, was suspended in July following a Water Tribunal appeal lodged by the coalition citing discrepancies in the granting of the licence.
Coalition spokesman Hayley Komen said the minister's discretion to lift the suspension should be exercised only in extraordinary circumstances, which in this instance did not apply.
The coalition fears that Molewa's decision will enable other companies to apply to have the suspension of their licence rescinded.
But Water Affairs spokesman Linda Page said Coal of Africa had pleaded with Molewa to be allowed to continue mining because the appeal against the suspension might take a long time. The lengthy suspension would have a negative effect on mining operations, revenue and the workers, she said.
Page said that the coalition's concerns were covered by the licence conditions and it would be involved in the monitoring of the water resources during mining operations.
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