Athletics South Africa (ASA) boss Chuene admitted Saturday that Semenya had undergone gender tests in South Africa before the world championships in Berlin, where she won gold in the 800 metres last month.
The ASA organised the tests at the request of world athletics body IAAF because of questions over Semenya's masculine build and rapidly-improved times over the past year.
"Chuene has not only lied to us as the ministry but to the whole country and this is not acceptable," Deputy Sports Minister Gert Oosthuizen said in a statement.
While Chuene insisted he lied to protect Semenya, Oosthuizen found that his lies "fuelled the continuous violation of Semenya's rights and dignity, by foreign and some local media" and called on ASA to fire him.
Before Saturday Chuene had persistently denied all knowledge of the tests, even as details of the intimate gynaecological tests performed on Semenya, and claims that she was duped into taking the tests, were splashed across local media.
Chuene acknowledged he had made "an error of judgement".
Chuene also revealed that South Africa's team doctor recommended that Semenya be withdrawn from the championships on the basis of the tests but that Chuene had refused, saying he did not want to deny her a shot at a medal on the basis of "rumours".
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