The 30-year-old, tested positive for testosterone but on Thursday insisted he was not a drugs cheat.
"No, c'mon man," Landis told Sports Illustrated website SI.com when asked if he did it.
The Phonak team also insisted that he would be sacked if the B sample confirmed the result.
Landis, the third American to win the race, could also become the first champion in the history of the Tour de France to be stripped of his title.
He said he "can't be hopeful" that the B sample would clear him. "I'm a realist," he said. "I wouldn't hold it against somebody if they don't believe me."
Ethics code must be applied: team
Phonak team boss John Lelangue told AFP he still had faith in Landis but would be obliged to apply the team's ethics code.
"We are surprised by the result but we will apply the procedure of the ethics code that we have signed," he said.
"If the result from the B sample confirms the first result, there will be dismissal."
The Swiss-based team said in a statement that it was notified by the International Cycling Union (UCI) on Wednesday of "an unusual level of Testosterone/ Epitestosteron ratio in the test made on Floyd Landis after stage 17 of the Tour de France."
More controversy for Tour
The news comes after a drugs scandal rocked the Tour on the eve of the race, which saw nine riders barred from competing.
The banned riders included pre-race favourites Jan Ullrich and Ivan Basso, who were implicated in a Spanish blood-doping ring.
It was the latest in a series of high-profile drugs controversies to tarnish cycling over the past decade, with the Tour de France being particularly hard hit.
The 1988 Tour de France champion Pedro Delgado tested positive but was never punished because the substance, probenecide, found in his urine was not prohibited at the time although it was on the Olympic list of banned substances.
Pound calls for UCI action
The leader of the World Anti-Doping Agency, Dick Pound said the controversy surrounding Floyd Landis' positive test shows how much work cycling has to do to restore its credibility.
The WADA chief, who is a frequent critic of cycling's doping record, said the sport's tainted image will be severely damaged if Landis' backup test confirms the positive finding for abnormal levels of testosterone.
"When is this going to end? What is the UCI going to do about it?" he said.
Pound said it was amazing that an athlete could risk doping during the Tour de France following the pre-race scandal.
"It's always disappointing when you see something like this," Mr Pound told The Associated Press by telephone from Montreal. "If there is a positive test, what have you got? The guys who came second, third, fourth, fifth and sixth at last year's event have been busted in the (Spanish investigation), and now the winner of this year's event is busted in the race itself."
Pereiro hopes Landis is clean
Landis claimed victory after a staggering 130km solo breakaway, a day after he had collapsed on the 16th stage and had tumbled down to 11th place overall, 8:08mins behind Spaniard Oscar Pereiro.
The Spaniard, who finished second overall, will be promoted to champion if Landis is kicked out.
"I would prefer to keep second place and that the first dope test wasn't confirmed," admitted the Caisse d'Epargne-Iles Baleares team rider.
Tour de France organisers said they were stunned by the news and a statement said: "If the B sample test confirms the first result, anger and sadness will dominate the feelings of all of those who had been filled with enthusiasm for the Tour de France of 2006."