Sources below. But first: I erred when I referred to the 800 meter world championship Semenya won in Berlin in August 2009 as the Juniors. It was the Women's World Championship. Semenya had already won the Junior (girls) Championship in the 800 the previous year.

Video of the August 2009 800m Women's World Championship, which Semenya handily wins by a huge margin: https://youtu.be/MpblUehi9Dk

Now the (main) sources:

1) Associated Press report on the press conference the head of ASA gave on September 19, 2009 admitting Semenya had been medically checked out in Pretoria on August 7, and that he and other officials decided to lie about it:

South Africa's top athletics official admitted on Saturday that he had denied knowledge of gender tests done on runner Caster Semenya in South Africa, saying he had lied to protect the athlete's privacy.

Athletics South Africa (ASA) president Leonard Chuene told reporters in Pretoria on Saturday that his constant denials of the tests, which he said he was aware of when they were done in early August, were an "error of judgment" and he hadn't meant to deceive the public.

"At that time I was acting in the best interests of Caster Semenya, as a person. I believed at that time that my consistent denials would help to protect her, that's what I believed. I have however realised that it was an error of judgment and that I could have been more forthcoming with this information, even if it was difficult," he said.

South African officials had repeatedly insisted tests were done on the 800-metre world champion only abroad, not in South Africa.

The International Association of Athletics Federations (IAAF) ordered more tests done on the runner in Berlin, saying questions had been raised about her muscular physique, running style and recent stunning improvement in times.

It has refused to confirm or deny Australian media reports that Semenya has both male and female characteristics, saying it was reviewing test results and would issue a decision in November on whether the athlete would be allowed to continue to compete in women's events.

Chuene admitted tests had been done at a Pretoria hospital on August 7 at the behest of the IAAF, adding that it was unclear whether Semenya was informed of the nature of the examinations.

Chuene said that despite medical advice and a request from the IAAF, he had refused to withdraw Semenya from the race because there were no results yet from the tests.

Video and text here: https://youtu.be/mLoTmod2jno

2)"Caster Semenya's Saga" by Ross Tucker, who is South African, published December 31, 2009 on science of sport:

Inside athletics circles, it has been widely known for about three years that all was not well with Semenya. In fact, three years ago, at the SA Junior Championships, ASA (Athletics South Africa, the official governing body) officials informed all competing teams that they knew of the problem and were investigating, so they should please not lodge any protests. Needless to say, nothing was done, until the IAAF acted on these reports, and requested an investigation from ASA (which is what they should do, according to their own policy).

ASA complied, under the guise of doping control, and Semenya found herself undergoing invasive physical examinations in South Africa, a few days before the team left for Berlin. Those results were enough to cause the ASA doctor, Harold Adams, to request that Semenya be withdrawn from the team. We may never know what was found by those tests. However, it is relatively easy to perform physical exams to confirm that an individual possesses no womb and has ambiguous genitalia. Genetic testing would follow and the picture would become clear very quickly. I would be very surprised if ASA did not know everything at that point. However, they refused to withdraw her, and the rest is history.

After a leading medical expert from a major SA university weighed in and told SA sports official to withdraw Semenya

Leonard Chuene (head of Athletics South Africa) publicly announced that he would not accept the opinion of a “scientist from some stupid university”, which tells you all you need to know about the now former president of ASA. Meanwhile, the Minister of Sport, our highest ranking sports official, declared that the questions about Semenya meant nothing. His words? “That means nothing. There are many hermaphrodites in the world so what does it matter. This girl is running as a girl who has been accredited as a girl. Nobody has questioned that (this comes after the whole world was questioning it, I might point out). She doesn’t have a womb, so what?”.

He went on to declare that if anyone tried to take her medal or stop her from running, it would be the “Third World War”. I was embarrassed to be South African, and wrote as much, for which I received a letter from the Minister saying that if I knew something he didn’t, I should say so. Perhaps the Minister will in future consult an expert endocrinologist, geneticist or doctor? Or maybe he’ll even read this website in 2010…

https://sportsscientists.com/2009/12/number-1-caster-semenya/

However, I would recommend reading all of Ross Tucker's posts on the Semenya case going in chronological order starting in August 2009. It's really an amazing story full of intrigue, outright lying, political bullying, PC posturing, and cowardice on the part of the IAAF and other sports bodies who to avoid charges of racism and sexism, backed off on the Semenya case in hurry then bent over backwards to come up with new rules to allow males with DSDs to compete in female sports.

3) "Semenya wins 800 meters" - report from ESPN, August 19, 2009, containing such doozies as:

South Africa team manager Phiwe Mlangeni-Tsholetsane would not confirm that Semenya was having a gender test, but said "there was no cheating on our part."

"We entered Caster as a woman and we want to keep it that way," Mlangeni-Tsholetsane said. "Our conscience is clear in terms of Caster. We have no reservations at all about that."

And this pack of lies from a spokesman for the University of Pretoria:

Morris Gilbert, a media consultant for TuksSport, the University of Pretoria's sports department, said the issue of Semenya's gender has not been raised since the 18-year-old freshman began attending the university.

"It's the first time in South African sport that we have had a gender issue," he said.

He said the university would not get involved in the recent controversy over her gender.

"We are all very proud of her and of what she's achieved," he said. "The university stands behind her all the way."

He attributed her recent success to hard work and rigorous training.

"She trains a lot," he said...

https://www.espn.com/olympics/news/story?id=4409318

4) "South African official lied about Semenya gender tests" - CNN report, September 19, 2009

https://edition.cnn.com/2009/SPORT/09/20/athletics.caster.semenya.chuene.oosthuizen/index.html

Some other relevant press reports:

https://www.espn.com/olympics/trackandfield/news/story?id=4489230

https://www.espn.com/olympics/trackandfield/news/story?id=6135110

Two corrections of errors I made in previous posts:

1) I believe the doctor I was referred to as Mandela's physician is Harold Adams (mentioned by Ross Tucker above). But it looks like Adams was the personal physician of two of the men who became President of South Africa after Mandela - Thabo Mbeki and Jacob Zuma - not Mandela. Though my recollection is that Mandela's physician weighed in too - this was a BIG topic in SA medical circles back in 2009. My notes say he did, but I can't find the source at the moment, so maybe I got that wrong.

https://www.pressreader.com/south-africa/mail-guardian/20090918/281535107030375

2) I said it was the head of Athletics South Africa who made the flip public statement about Semenya not having a womb, who cares? It was actually the SA Minister of Sport, as Tucker says. Not being from SA myself, I conflated the two positions. Apologies.