Chuene also admitted that he had lied to the South African public about not having any knowledge of gender tests conducted on Semenya in Pretoria last month.
He added that ASA's deception on the matter was intended to protect Semenya's confidentiality.
"I now realise that it was an error of judgement and I would like to apologise unconditionally. As president of ASA I will not, however, apologise for allowing caster Semenya to run or for protecting her privacy.
"We fully agree that we could have handled this matter differently but something like this has never happened in this country before and we at ASA believe we acted in the best interests of the athlete," he said.
But while Chuene was advised by Adams to withdraw Semenya, he said he refused to do so without any concrete evidence. He said that Adams' verbal recommendation was not sufficient for him to make a decision on such a sensitive matter.
Chuene also said that Adams, who travelled with Semenya to Berlin, should have advised the athlete to withdraw herself from the championships.
The IAAF is still awaiting the results of gender tests conducted in Berlin but Chuene said he would not accept those results because the world governing body did not follow the correct protocol.
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