Smith, now Michelle de Bruin, was banned for four years in 1998 after testing positive for an anabolic steroid.
Ye, 16, stunned world swimming on Saturday by winning gold and breaking the world record in the 400-meter individual medley. She swam the final 25 meters of her race faster than American Ryan Lochte swam the final 25 meters in winning gold in the men's 400-meter.
According the Daily Mail, Leonard, who is the executive director of the World Swimming Coaches Association, said the 16-year-old's performance was "suspicious" and "flat out impossible".
Shiwen denied suggestions that she might have used performance-enhancing substances.
"There's absolutely no problem with the doping," Ye said on Monday, the Los Angeles Times wrote.
"The Chinese team has always had a firm policy about doping," she said.
Leonard said "we want to be very careful about calling it doping," but added: "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.
Leonard, who said Ye "looks like superwoman" added: "Any time someone has looked like superwoman in the history of our sport they have later been found guilty of doping."
The Guardian wrote that his comments are likely to further increase tensions between China and the Americans. China poured vast amounts of resources into its sporting programmes in recent years and topped the US in the medal table for the first time in Beijing four years ago.