Alexandre Vinokourov tested positive for a banned blood transfusion after winning last weekend's time trial, prompting his Astana team to pull out and sending police on a raid of the team hotel.
Tour director Christian Prudhomme said the drug case showed cycling's testing system doesn't work.
"It's an absolute failure of the system," he said. "It is a system which does not defend the biggest race in the world. This is a system which can't last."
Tour leader Michael Rasmussen is also battling doping suspicions because he skipped drug controls before the Tour start.
"It's almost impossible to be at the front of the pack these days without doping," said Dick Pound, president of the World Anti-Doping Agency and a frequent critic of the way cycling is managed.
Vinokourov had been considered a pre-race favorite to win but crashed in the first week of the race. With stitches in both knees, he struggled for a few days but recovered to win stages Saturday and Monday - a turnaround that now seems too good to be true.
His positive test was announced by his team, whose manager, Marc Biver, said Vinokourov was sent home. The backup B-sample test results were expected by the end of the week.
"Alexandre denies having manipulated his blood," Biver said, adding that the rider believed his crash may have resulted in "blood anomalies in his body."
LANCE ARMSTRONG: Because of his former team's strong performance, Armstrong is considering making an appearance at the race, which he previously had planned to skip.
Tracking the 94th Tour
Tuesday: Rest day
Yellow jersey: Michael Rasmussen of Denmark
Today's stage: The third and final day in the Pyrenees is a 135.8-mile ride from Orthez to Gourette-Col d'Aubisque.
TV: 6:30 a.m., Versus