The Times also reported that the ASA had arranged the gender tests in Pretoria Aug 7 at the IAAF's request. Semenya's ex-coach Wilfred Daniels resigned last week after also claiming ASA had subjected her to the gender testing without her knowledge.
Chuene has denied the allegations, which if confirmed would amount to a serious breach of the athlete's rights, experts say.
The public scrutiny of Semenya's body has sparked anger in South Africa, where politicians, civil society groups and ordinary people have rallied to her side.
According to South African sports officials, she is only one of around four or five athletes who have undergone IAAF gender tests over the past year - but hers is the only case that was made public.
Sydney's Daily Telegraph on Friday reported that the tests had shown Semenya to have internal testes instead of ovaries, no womb and high testosterone levels. The IAAF is refusing to release the results until November, saying it wants to speak to Semenya and consult experts first.
The South African government has accused the IAAF of violating Semenya's rights and vowed legal action against the IAAF, warning any attempt to ban her from competition would lead to a 'third world war.'
The Johannesburg law firm that represented double-amputee sprinter Oscar Pistorius in his successful challenge against an IAAF ban last year has taken on the case.
Semenya has gone to ground since Friday's 'hermaphrodite' revelations. She pulled out of a race in Pretoria Saturday.