American John Leonard, who is the executive director of the World Swimming Coaches Association, said that the final length of 16-year-old Ye’s world record time of 4:28.43 was “unbelievable” and “disturbing”.
He pointed to her freestyle split of 58.68sec, which boasted a last 50m of 28.93s that was quicker than men’s champion Ryan Lochte managed in the equivalent race (29.10s), highlighting that the rest of Ye's race was not extraordinary until that point.
Leonard, an outspoken advocate of drug-free sports, referenced her sudden improvement in that leg, where she moved from her standard six-beat kick in the heats to an eight-beat kick to surge past the opposition.
"We want to be very careful about calling it doping," Leonard told The Guardian. "The one thing I will say is that 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.
“No woman has ever split the men, let alone the two greatest all-rounders (Michael Phelps and Lochte) in the history of the sport.”
“That last 100m was reminiscent of some old East German swimmers, for people who have been around a while. It was reminiscent of the 400m individual medley by a young Irish woman in Atlanta."
Leonard was referring to Michelle Smith, now De Bruin, who was later banned for doping offences. The 1990s also saw more than 40 positive tests for Chinese swimmers.
But Ye, who stands at 5'8" which is not tall for a female swimmer, insisted that she is clean.
“My results come from hard work and training,” she was later quoted as saying.
“I wouldn’t use any banned drugs. The Chinese team has always had a firm policy about anti-doping.”
In questioning Ye’s achievements, Leonard pointed to the standard markers for doping: sudden and marked improvements in overall performance, and the appearance of an athlete working within themselves before finding an exceptional burst past his or her rivals.
"Any time someone has looked like superwoman in the history of our sport they have later been found guilty of doping,” he added.
“The final 100m was impossible. Flat out. If all her split times had been faster I don't think anybody would be calling it into question, because she is a good swimmer. But to swim three other splits at the rate that she did, which was quite ordinary for elite competition, and then unleash a historic anomaly, it is just not right.
"I have been around swimming for four-and-a-half decades now. If you have been around swimming you know when something has been done that just isn't right. I have heard commentators saying 'well she is 16, and at that age amazing things happen'. Well yes, but not that amazing. I am sorry.”
Leonard also rejected that he was playing to a stereotype of Chinese athletes, pointing to men’s champion Sun Yang as a swimmer who is probably clean.
"You can't turn around and call it racism. The China have a doping history. You have to question any outrageous performance, and that is an outrageous performance, unprecedented in any way, shape or form in the history of our sport. It by itself, regardless of whether she was Chinese, Lithuanian, Kenyan, or anything else, is impossible. Sorry.
"Sun has a perfectly normal improvement curve, he is a dramatically spectacular athlete in our sport and I've no question about him at all.
“But a woman does not out-swim the fastest man in the world in the back quarter of a 400m IM that is otherwise quite ordinary. It just doesn't happen."
Leonard also pointed out that Michael Phelps, who broke the world 200m butterfly record at 15, had kept to a consistent trajectory of improvement that tallies with natural growth and training work.
He even suggested that doping in its traditional form may not be at play – but that genetic manipulation was an option that testing authorities would have to consider.
"I am sure that Fina and the doping authorities have taken every sample they can take," he added.
"The sample will be tested and available for testing for the next eight years. And over eight years, if there is something unusual going on in terms of genetic manipulation or something else, I would suspect over eight years' science will move fast enough to catch it.
"I have every faith that eventually if there is something there to be caught it will be caught. Right now all we can say is Olympic champion, world record holder, and watch out for history.”
Ye was also the fastest qualifier for the 200 individual medley final later, setting an Olympic record in qualifying. She has not, however, been entered for the freestyle events.
Asked whether Ye's doping test had come in positive or negative, IOC spokesman Mark Adams said: "We would only comment if we had any adverse finding. I am not commenting, so you can draw your own conclusions.
"I think we need to get real here. These are the world's best athletes competing at the highest level."
Adams said the first five athletes in each event were tested and two others as well.
"We have a very, very strong drugs testing programme," he said. "If there are cheats we will catch them.
"You cannot stop speculation," Adams said. "It is something that people talk about. It is a sad result of the fact that there are people who cheat. If you cannot applaud a good performance let's give the benefit of the doubt."