Semenya's feet were apparently placed in stirrups as photographs were taken of her private parts that left her "bitterly upset".
The incident is believed to have happened during her country's athletics trials on August 7, and she thought she was going to hospital for drug tests.
Wilfred Daniels, the former head coach of Athletics South Africa (ASA), was quoted as saying: "The tests took almost two hours.
"Semenya became frustrated and even angry over the humiliating nature of the tests."
She called and sent text messages to friends from the Pretoria hospital to tell them about her ordeal, the South African newspaper Beeld said.
The governing body of world athletics, the IAAF, ordered separate gender tests on Semenya after she convincingly won the women's 800 metres final at the world championships on August 19.
The results are not yet known but the IAAF declined to confirm last week's report in Australia's Daily Telegraph that the 18-year-old had both male and female sexual characteristics.
Some South Africans have accused the organisation of racism for ordering the tests.