Ye, who won two golds at the London Games, set a world record in the 400 metres individual medley and shaved five seconds off her personal best, instantly raising questions given her country's doping past.
Leonard, executive director of the World Swimming Coaches Association, said history showed that every time something "unbelievable" occurred in the sport it turned out ultimately to involve doping.
While the United States Olympic Committee distanced itself from his remarks, and there was no evidence to show Ye's performance was down to doping, the case kicked off a firestorm in China with many seeing the accusations as biased and racist.
"The coach (Leonard) was not professional," Xinhua quoted Ye as saying on Friday.
"If a foreign swimmer achieved this result they may say it is a miracle," the 16-year-old added. "I won't be affected by any accusations."
Ye trailed world champion Elizabeth Beisel of the US after the penultimate breaststroke leg in her individual medley before producing a devastating finish over the final two freestyle lengths.
The Chinese teenager covered the penultimate lap in 29.75 seconds, faster than record-breaking Michael Phelps in the men's final, and the last in 28.93, quicker than Ryan Lochte did in winning the male equivalent.
"How can I be compared with Lochte?" Ye asked. "His 400 result was more than 20 seconds faster than mine and he was totally relaxed over the last part of the race.
"I was trying my best to come from behind. Freestyle was my favourite in the medley but I still cannot be compared with professional men's freestylers.
"A freestyle turn is different from breaststroke-to-freestyle transition and the former is much faster than the latter," Ye added. "It's normal the last 50 in the 200 medley is slower than that in the 400 medley."
She said that now her Games was over all she wanted to do was sleep.
"Because of doping tests and press conferences I went back to my room very late," said Ye. "As the competition is over I can finally have a good sleep."
Writing on her Sina Weibo microblog on Thursday, Ye gave a sarcastic thanks to the Western media which had also cast aspersions over her successes.
"A really big thanks to everyone for their support! Including the doubts from the Western media!" she said.
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