Jean-Marie Leblanc, the Tour's director general, told The Associated Press that Millar, his teammate Cedric Vasseur and a half-dozen lesser-known riders from three other teams were not welcome at this year's showcase race, which starts July 3.
"We don't want to pollute the Tour," Leblanc said.
Millar is the highest-profile casualty of a decision announced Friday by Tour organizers that all riders implicated in judicial or police doping probes will be barred from the three-week race.
Cycling's governing body, the UCI, approved the measure, organizers said.
Leblanc said the decision concerns Millar's Cofidis team, as well as the Fassa Bortolo, Domina Vacanze and Saeco squads.
"Eight days ago, we warned their leaders that we didn't want riders implicated (in probes) on the Tour," Leblanc said in a telephone interview. "At Cofidis, that concerns Vasseur and Millar."
The British cyclist, the defending world time trial champion on road, spent two days in police custody this week. A well-placed judicial official said Millar was questioned about allegations that he distributed doping products during last year's race, where Texan Lance Armstrong won for a fifth straight time.
Millar admitted during the police questioning that he has taken the endurance drug EPO, which works by boosting oxygen-carrying red blood cells, during his career, without specifying exactly when, said a police official who spoke to the AP on condition of anonymity.
Police also found two used syringes labeled Eprex 4000, a form of EPO, in a search of Millar's home in the southwestern town of Biarritz, said another police official. The syringes are being analyzed, he said.
If Millar was doping just weeks before the Tour, it could cast new doubt on the effectiveness of drug controls. As a star rider with a chance of winning time trials, Millar could have been tested. But if he was taking EPO, that could suggest he did not think tests would catch him.
Millar won the final time trial on last year's Tour.
Leblanc said Millar would not race this Tour, "as with all riders who are involved either in judicial or police affairs."
"We want a peloton that is as transparent as possible," the Tour director said.
"We don't want to pollute the Tour. We want the race to run serenely and not be contested from the start," Leblanc added.
Asked whether Millar denies the allegations against him, his manager and sister Fran Millar said: "This is obviously a legal investigation and the French lawyers have to speak to David."
There was no reply Friday to repeated calls to the only telephone number listed in Biarritz for a David Millar.
The doping scandal surrounding Cofidis is the biggest to hit the sport since the 1998 Tour de France almost ground to halt amid police raids and the arrest of an assistant for the Festina team found with a stash of drugs in his car.
Armstrong and his U.S. Postal Service team have not been implicated in the French investigation centering on Cofidis. But the Texan has had to defend himself against a new book, L.A. Confidential, The Secrets of Lance Armstrong, that insinuates, without providing ironclad proof, that he has doped.
Armstrong is taking legal action against the authors and has repeatedly insisted that he is clean.
The Texan, who came back from cancer to first win in 1999, is shooting for a record sixth Tour crown this year.
Leblanc, the Tour director, took the latest developments stoically.
"Since 1998, we've grown used to books coming out and (television) programs being made on the theme of doping each year in June. And we've become accustomed to justice and police operations being launched," he said. "It's unpleasant."
But he said "the great majority of riders" at the start next week in Liege, Belgium, "will be worthy of participating in the Tour."