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 reports.
And she could be stripped of the gold medal she won in Berlin in last month, as she has three times more testosterone than a normal female.
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.
It is believed that Semenya is unaware the tests has identified her as a hermaphrodite.
Only the certainty of a backlash from South Africa has so far prevented the IAAF from banning Semenya and revoking her gold medal.
South Africa embraced the feisty teenager after the storm of controversy from Berlin, declaring her "Our girl".
African National Congress MP and National Assembly sports committee chairman Butana Komphela has already lodged a complaint with the United Nations High Commission on Human Rights, accusing the IAAF of racism and sexism.
The IAAF expects to receive the full set of results this week. (ANI)