Semenya was asked to take a gender test at the end of July
An inquiry has been ordered into the way the decision to make Caster Semenya take a gender test became public.
The 18-year-old South African won the 800m at the World Athletics Championships but tests to prove she was female were ordered.
Lamine Diack, president of the International Association of Athletics Federations, said: "I regret that confidentiality was breached.
"It is an unfortunate matter and I have requested an internal inquiry."
Three weeks before the World Championships, the IAAF asked for gender tests to be carried out amid fears that she should not be allowed to run as a woman.
But that only became public after Semenya had won gold in Berlin in a year's best 1:55.45.
Diack added: "The IAAF were forced into a position of having to confirm that gender testing was being carried out on this young athlete. I want to ensure that procedures are tightened up and this never happens again."
Britain's Jenny Meadows, who finished third behind Semenya to win the bronze medal, said she sympathised with the South African.
She said: "I just feel sorry for Caster. It's not a nice position to be in. It's for the IAAF and South African federation to sort that out. I don't think she should have been put in that position at all.
"She didn't make much eye contact with anybody. I think she was half-embarrassed by the whole situation herself. I just really feel for her. It's a situation that could have been avoided."