The samples contained synthetic testosterone, indicating that it came from an outside source.
"I have received a text message from Chatenay-Malabry lab that indicates the 'B' sample of Floyd Landis' urine confirms testosterone was taken in an exogenous way," Pierre Bordry, who heads the French anti-doping council, told The Associated Press shortly after the "B" sample results were released.
Lab head Jacques De Ceaurriz said the isotope testing procedure was "foolproof."
"No error is possible in isotopic readings," he told the AP.
Landis, of Murrieta, Calif., had claimed the testosterone was "natural and produced by my own organism," and once again maintained his innocence.
"I have never taken any banned substance, including testosterone," he said in a statement. "I was the strongest man at the Tour de France, and that is why I am the champion.
"I will fight these charges with the same determination and intensity that I bring to my training and racing. It is now my goal to clear my name and restore what I worked so hard to achieve."
But Dr. Gary Wadler, an expert on athlete drug use, told CBS News correspondent Randall Pinkston that it's unlikely Landis will be able to prove his innocence. "Something happened the day he tested positive. Somehow testosterone levels shot up and they don't just shoot up from changes in your own body."
The Swiss-based team Phonak immediately severed ties with Landis, and the UCI said it would ask USA Cycling to open disciplinary proceedings against him.
"Landis will be dismissed without notice for violating the team's internal Code of Ethics," Phonak said in a statement. "Landis will continue to have legal options to contest the findings. However, this will be his personal affair, and the Phonak team will no longer be involved in that."
Tour de France director Christian Prudhomme said Landis no longer was considered champion, but the decision to strip him of his title rests with the International Cycling Union.
"It goes without saying that for us Floyd Landis is no longer the winner of the 2006 Tour de France," Prudhomme told the AP in a telephone interview. "Our determination is even stronger now to fight against doping and to defend this magnificent sport."
Prudhomme said runner-up Oscar Pereiro of Spain would be the likely new winner.
"We can't imagine a different outcome," Prudhomme said.
If stripped of the title, Landis would become the first winner in the 103-year history of cycling's premier race to lose his Tour crown over doping allegations.