The Phonak team suspended Landis, pending results of the backup "B" sample of his drug test. If Landis is found guilty of doping, he could be stripped of the Tour title, and Spain's Oscar Pereiro would become champion.
It wasn't immediately known when the backup sample will be tested.
The Swiss-based Phonak team said it was notified by the International Cycling Union (UCI) on Wednesday that Landis' sample showed "an unusual level of testosterone/epitestosterone" when he was tested after stage 17 of the race last Thursday.
"The team management and the rider were both totally surprised of this physiological result," the Phonak statement said.
Efforts to reach Landis were not immediately successful.
The 30-year-old Landis made a remarkable comeback in that Alpine stage, racing far ahead of the field for a solo win that moved him from 11th to third in the overall standings. He regained the leader's yellow jersey two days later.
Landis rode the Tour with a degenerative hip condition that he has said will require surgery in the coming weeks or months.
Arlene Landis, his mother, said Thursday that she wouldn't blame her son if he was taking medication to treat the pain in his injured hip, but "if it's something worse than that, then he doesn't deserve to win."
"I didn't talk to him since that hit the fan, but I'm keeping things even keel until I know what the facts are," she told The Associated Press in a phone interview from her home in Farmersville, Pennsylvania. "I know that this is a temptation to every rider but I'm not going to jump to conclusions ... It disappoints me."
The Phonak statement came a day after the UCI, cycling's world governing body, said an unidentified rider had failed a drug test during the Tour.
Phonak said Landis would ask for an analysis of his backup sample "to prove either that this result is coming from a natural process or that this is resulting from a mistake."
Phonak said Landis has been suspended and that he will be fired if the second sample confirms the initial finding.
USA Cycling spokesman Andy Lee said that organization could not comment on Landis.
"Because it's an anti-doping matter, it's USA Cycling's policy not to comment on that subject out of respect for the process and Floyd's rights," Lee said. "Right now, we have to let the process proceed and we can't comment on it."
Carla O'Connell, publications and communications director for the U.S. Anti-Doping Agency, said: "I'll make this very brief: No comment."
UCI spokesman Enrico Carpani said Landis was notified of the test Wednesday morning. He said the cycling body doesn't require analysis of the "B" sample, but that Landis requested it.
"We are confident in the first (test)," Carpani said. "For us, the first one is already good."
Under World Anti-Doping Agency regulations, a ratio of testosterone to epitestosterone greater than 4:1 is considered a positive result and subject to investigation. The threshold was recently lowered from 6:1. The most likely natural ratio of testosterone to epitestosterone in humans is 1:1.
Testosterone is included as an anabolic steroid on WADA's list of banned substances, and its use can be punished by a two-year ban.
Landis wrapped up his Tour de France win on Sunday, keeping the title in U.S. hands for the eighth straight year. Lance Armstrong, long dogged by doping whispers and allegations, won the previous seven. Armstrong never has tested positive for drugs and vehemently has denied doping.
On Thursday, Armstrong was riding in RAGBRAI, an annual bike ride across Iowa that attracts thousands of riders.
At the first break in Sully, Iowa, about 50 miles southeast of Des Moines, Armstrong had little to say at the Coffee Cup Cafe, where he grabbed a slice of coconut cream pie and a big glass of ice water.
When asked about Landis, Armstrong told The Associated Press: "I'm not here to talk about that."
Landis' inspiring Tour ride reminded many of fellow American Tyler Hamilton's gritty 2003 performance. Hamilton, riding for team CSC, broke his collarbone on the first day of the Tour but rode on, despite the pain, and finished fourth overall.
But, a year later, Hamilton, then riding for Phonak, tested positive for blood doping at a Spanish race and now is serving a two-year ban. He has denied blood doping.
Speculation that Landis had tested positive spread earlier Thursday after he failed to show up for a one-day race in Denmark on Thursday. A day earlier, he missed a scheduled event in the Netherlands.
On the eve of the Tour's start, nine riders - including pre-race favorites Jan Ullrich and Ivan Basso - were ousted, implicated in a Spanish doping investigation.
The names of Ullrich and Basso turned up on a list of 56 cyclists who allegedly had contact with Spanish doctor Eufemiano Fuentes, who's at the center of the Spanish doping probe.
World Anti-Doping Agency chief Dick Pound, speaking before Landis was confirmed as the rider with the positive test, said it was amazing any cyclist would risk doping after the scandals that rocked the Tour before the start.
"Despite all the fuss prior to the race with all these riders identified and withdrawn, you still have people in that race quite willing and prepared to cheat," he told the AP by phone from Montreal. "That's a problem for cycling."
