She spoke out after a leading US coach described her performance in the 400m individual medley as "disturbing".
Ms Ye swam the 400m individual medley seconds faster than she ever had before and - on the last 50m - faster than the winner of the men's event.
There is no evidence against her and all medal winners are drug-tested.
On Monday, Ye Shiwen took at least five seconds off her personal best to break the world record by more than a second and win the gold medal in the individual medley.
In the last 50m she swam faster than US star Ryan Lochte in the men's event.
Commentators were stunned, including the BBC's Clare Balding who said questions would be asked about the swimmer's performance.
John Leonard, executive director of the World Swimming Coaches Association, said her performance was "unbelievable" and "disturbing".
However, Arne Ljungqvist, medical commission chairman for the International Olympic Committee, called the speculation "sad".
"To raise suspicion immediately when you see an extraordinary performance - to me it is against the fascination of sport," he said.
When asked about the suspicions, Ye Shiwen told reporters: "My results come from hard work and training and I would never use any banned drugs. The Chinese people have clean hands."