The International Association of Athletics Federations says it demanded the test three weeks ago amid fears she should not be able to run as a woman.
IAAF spokesman Nick Davies said the "extremely complex, difficult" test results were not due for several weeks.
The South African athletics federation insists it is "completely sure" that Semenya, 18, is a female.
"We would not have entered her in the female competition if we had any doubts," said a statement.
Semenya won gold in impressive fashion on Wednesday, leaving her rivals trailing as she won in a time of one minute, 55.45 seconds.
Defending champion Janeth Jepkosgei was second, a massive 2.45 seconds adrift, with Britain's Jenny Meadows taking bronze.
Semenya did not attend a post-race news conference following her success, but IAAF secretary general Pierre Weiss did appear before the media.
"We know you want to talk to her, but she is young, she is inexperienced and she is not able to reply properly to all your questions," he said.
"I will answer for her. The decision not to put her up was taken by the IAAF and the South African federation.
"I repeat, she was not prepared for a situation like this."
Weiss insisted the IAAF had handled the situation as best as it could and defended the timing of the announcement to test Semenya.
"She was unknown three weeks ago," he said. "No one could have anticipated this. We are fast but we are not a lion."
He added: "If it is proved that she is not a female, she will be withdrawn and the medals revised. At the moment, the athlete must be given the benefit of the doubt."
Semenya burst on to the world stage when she ran 1.56.72 in Bambous last month, smashing her previous personal best by more than seven seconds.
She also broke Zola Budd's long-standing South African record and arrived here as the newly-crowned African junior champion.
"In the case of this athlete, following her breakthrough in the African junior championships, the rumours, the gossip was starting to build up," said Davies.
"The gender verification test is an extremely complex procedure. The situation today is that we do not have any conclusive evidence that she should not be allowed to run."
A group of doctors, including an endocrinologist, a gynaecologist, an internal medicine expert, an expert on gender and a psychologist, have started the testing procedure but it is uncertain when the results will be known.
Weiss said testing was being done in Berlin and South Africa but admitted it was a complex issue.
"At this stage, it's confusing," he said. "Personally I have no clue what's going on. I rely on and trust our doctors. We would have preferred not to have had a controversy."
After the race, Meadows said: "It's up to the IAAF to sort it out. You can't do anything about who is out there.
"There's just eight people on the track and you just have to make sure you're in the first three to get a medal."