Cyril Ramaphosa has denied involvement in the alleged intervention by Edna Molewa to prevent legal action against mining companies linked to him.
It was discovered that the companies were operating without water licences.
The Mail & Guardian last week quoted two senior department officials who confirmed that it had taken the Shanduka Group of companies to court and referred the matter to the National Prosecuting Authority.
Shanduka chief executive Phuti Mahanyele this week told the M&G that Ramaphosa had never held a discussion with Molewa about water licences. "While no direct allegations against Ramaphosa are made, the overall impression created by the article is that Ramaphosa improperly used political influence to benefit companies within the Shanduka Group.
Second, the claim that legal action was instituted against Shanduka Coal is incorrect. In fact, Shanduka Coal was issued with a directive by the water affairs department in May 2012 to present its water-use licence or cease operations at the affected mines within two days. This does not constitute legal action," said Mahanyele.
Mahanyele said the company had indicated its intention to launch an urgent high court application to interdict the issuing of any pending directive, review the unreasonable delay in making a decision on licences and compel the department to take a decision within a time period determined by the court.