Ye's stunning performance in the 400 metre individual medley, where she knocked five seconds off her previous best time, raised the eyebrows of a number of commentators, including a senior US coach, and suggestions that performance-enhancing drugs could have played a role.
She won her second gold of the Games in the 200m individual medley just a few days later, beating Australia's Alicia Coutts into second place.
Denis Cotterell, the former coach of Olympic gold medallist Grant Hackett, has trained Ye and other top Chinese swimmers.
He said he was "100 per cent certain" Ye was clean and said the questions over doping had been raised by people who do not understand the sport.
"You have to have a look at the improvements in Beijing," he told PM.
"If people do their homework and you have a look at some of the world records ... the margins that they have been dropped by some of the extremely talented swimmers that have applied themselves over the past – it is a combination of their talent and their work ethic."
Cotterell said Ye's five-second improvement to her personal best time was not a one-off.
"[There have] been great achievements by people in the sport, it's part of the history ... and talent comes along and makes a good drop and shocks a few people but we generally seem to have accepted it," he said.
"But for some reason in this case now, it's not, because of the Chinese [history]."
"Ian Thorpe, no one questioned, Michael Phelps, no one questioned. And having worked with the girl and seeing how hard she works and the talent she is, it is disappointing that the kid is in the media conference on her own with 100 journalists having to defend herself."
He said Ye's performance was all the more impressive considering the allegations against her and the high-pressure nature of the Games.
"It's very sad that she's having to go through that," he said.
"This Olympics is a very, very tough meet and it makes what she has been doing even more amazing under the microscope that she's been placed under and the allegations."
"You just have to look and see what the pressure of competition does to a lot of swimmers, including our own James Magnusson."
And he described Ye's critics as "quite ignorant".
"If it was your own daughter and you had seen what she had sacrificed over a large number of years, then to finally make this achievement they have seen what she has been through and now, instead of acknowledging the result, there are allegations and questions."
He said Ye, who is also the 200m medley world champion, always had gold medal potential.
"She came back after working with us. She dropped her time another three seconds and another year of work on and she has moved her times forward again," he said.
"She was a great world-ranked swimmer at 14, she won the world title at 15. You would like to think there was room for improvement."
"[The Chinese swimmers are] brilliant workers and they apply themselves like most other people do not."