Senior American coach and prominent anti-doping advocate John Leonard was quick to voice his suspicions.
"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.
"That last 100m was reminiscent of some old East German swimmers, for people who have been around a while," said Leonard, who is executive director of the World Swimming Coaches Association. "It was reminiscent of the 400m individual medley by a young Irish woman in Atlanta."
Leonard's comments, especially the calculated reference to disgraced Irish swimmer Michelle Smith (later de Bruin) - who was banned for four years after winning three gold medals and a bronze at the 1996 Atlanta Games - prompted a storm of high-level indignation and counter-claims of racism.
Swimming's governing body, Fina, said there was no factual basis to the accusations, as Ye had passed four doping tests in the past 12 months, including two before the Chinese Olympic trials this year.
International Olympic Committee spokesman Mark Adams retorted that critics needed to "get real", as the world's best athletes were bound to break records at the Olympics.
"It's very sad we can't applaud a great performance. Let's give the benefit of the doubt to the athletes."
China's anti-doping head, Jiang Zhixue, was among many who saw the criticism as anti-Chinese or racist.
"We never questioned Michael Phelps when he bagged eight gold medals in Beijing," Zhixue told Xinhua agency. "I think it is not proper to single Chinese swimmers out once they produce good results. Some people are just biased."
Phelps publicly agreed, saying he thought Ye's performance would have been reported very differently if she had been an American. And, as Ye went on to win the 200m individual medley and break the Olympic record the following day, her supporters pointed out that unlike Smith - who could not even qualify for top-level finals before her shock Atlanta wins - the Australian-trained teenage star was hardly an overnight sensation.
BORN IN Hangzhou, capital of China's eastern Zhejiang province, to a mother who was a champion long-jumper and a father who excelled at running, Ye reportedly took up swimming at an early age after her kindergarten teacher noticed her large hands and feet.
She progressed through the city's Chen Jinglun Sport School, which has produced past swimming and gymnastic champions, making the national team in 2008.
At the 2010 Asian Games she swam the year's fastest time for the 200m medley. Last year at the world championships in Shanghai she beat American world record-holder Ariana Kukors and Australia's Olympic champion Stephanie Rice in the same race, largely thanks to her now hotly debated freestyle finish.
Several former Olympic swimmers told the BBC that teenage swimmers could make huge improvements in their times, so Ye's seven-second improvement on last year's time was not impossible.
"The big question is over the way Ye swam in the last 50m," said Sharron Davies, who won silver in the same event at the 1980 Moscow Games. "That's what we're all finding a little bit difficult to take in. But [British swimmer] Becky Adlington's last 50m of the 800m [freestyle] was also quicker than Lochte's, so we have to be careful that we don't jump to ridiculous conclusions."
Adrian Moorhouse, a 1988 100m backstroke gold medallist, pointed out that no one was making doping accusations against 15-year-old Ruta Meilutyte, the shock winner of the 100m breastroke a day after Ye's breakthrough.
Meilutyte, who swims for Lithuania but lives in England, has become the blond-haired darling of the medal-hungry British tabloids. She set a new European record in her semi-final, spectacularly improving her time by a similar percentage to Ye, but without the controversy.
As one blogger, Dermot Hunt, sarcastically put it, the lack of outrage over Meilutyte's sudden improvement compared to Ye's was the real answer to BBC commentator Balding's provocative question.
"If you're white, if you have an English trainer, then everyone's going to be delighted for you. If you're Chinese, you're going to face a barrage of cowardly smears and insinuations that will ruin the greatest day of your life. Hurrah for the Olympics."
However, Leonard's views have strong support from sports scientist and international doping expert Ross Tucker, who said though the case against Ye was unproven, a degree of scepticism was justified.
Writing on his website, sportsscientists.com, Tucker said he was partly suspicious because Ye was a 16-year-old girl who had not only broken a world record but improved her time by seven seconds in an event in which she finished fifth last year.
She was also from China, which had a history of doping swimmers in the 1990s and a 16-year-old swimmer who tested positive for EPO this year.
"Does anyone who knows China's ethos and attitude towards Olympic sport actually believe that they would not deliberately dope their young athletes to win medals?" he asked. "If your answer is no, then I'm afraid you're naive."
Tucker said the key question was over Ye's speed on the freestyle leg of the medley, not just compared to Lochte's but to her peers and to the best 100m freestyle swimmers.
Medley swimmers were slower in freestyle than 100m specialists, so men typically did the 100m leg in 57 to 59 seconds, compared to 61 to 64 seconds for women. Both men and women were about 20 per cent slower in the medley than the best 100m freestyle swimmers.
Yet Ye was only 10 per cent slower than an unfatigued 100m freestyle specialist, suggesting she must have had considerable reserves of strength left after 300m.
He suspected Ye could probably swim two or more seconds faster overall - a "scary thought" - if she went out faster for the first 300 metres.
Drugfree Sport NZ chief executive Graham Steel said the question marks over Ye's astonishing swim were perfectly understandable.
"Those who have been around for a long time are inclined to be sceptical of performances that are just beyond - I suppose credibility or normal expectations of the progression of human performance.
"So there's reason to be questioning but at the same time there are occasions when there are phenomenal performances. One thinks of Bob Beamon setting world long jump records that lasted 20 or 30 years [the US athlete's remarkable 8.9m jump in the 1968 Mexico Games is still an Olympic record] and I'm not aware of doping being implicated there. That was just a sublime performance on the day."
Steel said one of the suspicious aspect's of Ye's performance was not the time itself but the fact that she swam as fast as the men, which was highly unusual. "If that occurred for a New Zealand performer ... we would be doubly vigilant around that person. That would become one of the triggers for us to pay extra-special attention."
Steel said it was normal for drug-testing bodies to focus on high-performing athletes in sports that were historically prone to doping. Leading up to the Olympics, Drugfree Sport NZ had a list of about 90 "priority athletes", mainly in power or endurance sports, who had to account for where they were each day. Some were also subject to a biological profile, which tracked changes in biological markers in their blood for future reference, even if there was no current evidence of a banned substance.
Steel added that despite its poor record in the 1990s, China had recently show a much greater willingness to work with international anti-doping programmes and ran a very good programme at the 2008 Beijing Olympics.
"They provide more confidence than they would have 10 years ago that they're trying to do the right thing."
And he urged people watching the Games on television not to become overly cynical about possible doping.
"We have very good faith in the fact that the New Zealand athletes are clean, for example, and that you can trust their performances. That's not a guarantee but we certainly have that confidence. A performance like this will inevitably bring about questions but I don't think we're at the point now where you should be questioning every performance at the Games - in fact, far from it."
