The 16-year-old’s success was marred by critics who expressed concern after she smashed her personal best and beat the world record during the 400m individual medley.
However Locog chairman Lord Coe said his instinct was to “celebrate an extraordinary performance”.
He added: “It is not the first time that teenagers have broken world records or won Olympic titles.
“You have got to be very careful when you suddenly assume that a massive and unexpected breakthrough in an event or a particular discipline is based on anything other than great coaching and extraordinary talent. I speak slightly from personal experience here, I remember in my late teen years I took four and a half seconds off my 800m personal best.
“So it is really not that unthinkable.
“My instinct is to always give benefit of the doubt to the competitor until proven otherwise. My instinct is to celebrate an extraordinary performance.”
He compared Shiwen’s success to that of sprinter Usain Bolt adding: “Nobody really noticed that until he explodes into a world championship or an Olympic stadium.”
Ye, who has claimed two gold medals, has firmly denied taking performance-enhancing drugs.
Critics expressed concern after she took five seconds off her personal best and more than a second off the world record in the 400m individual medley.
She then won the 200m individual medley.
Ye said: “I think that in other countries other swimmers have won multiple golds and no one has said anything.”