Lord Colin Moynihan said Ye, 16, had passed drug tests, was "clean" and deserved recognition for her talent.
Ye smashed her personal best by at least five seconds in the 400m Medley.
Senior US coach John Leonard said her performance was disturbing and hinted that doping could have been involved.
Mr Leonard, executive director of the World Swimming Coaches Association, said the performance reminded him of the East German women swimmers in the 1980s, who were doping on a systematic basis.
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"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.
But Ye, who will compete later in the 200m Medley final, has strongly defended herself and denied that she would ever use banned substances.
China's anti-doping chief has said that Chinese athletes have undergone nearly 100 drugs tests since arriving in London, and that not a single Chinese athlete had tested positive.
Former swimmers, other Olympic champions and experts have all given their support to Ye.
Lord Moynihan told a news conference that the World Anti-Doping Agency (Wada) was "on top of the game".
"She's been through Wada's programme and she's clean. That's the end of the story. Ye Shiwen deserves recognition for her talent," he said.
Former British Olympic champion Adrian Moorhouse said the rumours appeared to be a case of sour grapes.
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