Lord Colin Moynihan said Ye, 16, had passed drug tests, was "clean" and deserved recognition for her talent.
"History in our sport will tell you that every time we see something, and I will put quotation marks around this, unbelievable, history shows us that it turns out later on there was doping involved," he told the UK's Guardian newspaper.
A top US coach had called Shiwen "suspicious" and compared her to East Germany's drug-addled athletes after her super-fast times were questioned at the London Olympics.
John Leonard, executive director of the World Swimming Coaches Association, told The Guardian that the 16-year-old's lightning freestyle leg in her world-record 400m individual medley swim was simply "impossible".
The schoolgirl timed 58.68sec in the last 100 metres, a whisker off US winner Ryan Lochte's time in the men's competition.
Astonishingly, her final lap was quicker than the American champion.
China's anti-doping chief Jiang Zhixue said Chinese swimmers have undergone nearly 100 drug tests since they arrived in Britain for the Olympics.
"I think it is not proper to single Chinese swimmers out once they produce good results. Some people are just biased," he said.
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