The IAAF commissioned a gender test on the teenager after her performance levels improved remarkably in the build-up to the competition.
The tests, not yet publicly released, show the 18-year-old has no womb or ovaries.
The IAAF is expected to disqualify the South African from future events and advise her to have surgery because her condition carries grave health risks, The Daily Telegraph report claims.
A source closely involved with the IAAF tests said Semenya had internal testes -- the male sexual organs, which produce testosterone.
"There certainly is evidence Semenya is a hermaphrodite. But the trouble is the IAAF now has the whole ANC and the whole of South Africa on their backs. Everything is going to have to be done absolutely by the book, no question of a challenge to the findings," the source said.
The IAAF has responded by urging caution over the reports, The Independent reports.
"The IAAF has issued a statement that said the case will come before the executive council in November where it will be decided. They told us this week that the tests are inconclusive and they could not give us the results just yet. So I really do not know where the Australia media got this latest one from," Chuene said.
A statement released to Press Association Sport, read: "The IAAF can state that statements in the Australian press should be treated with caution as they are not official statements by the IAAF."
Chuene also rubbished local media claims earlier this week alleging that ASA was refusing to co-operate with the IAAF's request to be put in contact with Semenya ahead of the announcement of the controversial gender tests.
Speaking to The Star, Chuene also pointed out that the reports from Australia were likely to have a psychological effect on Semenya. (ANI)