Police made their move on the Tour's first rest day in arresting Cofidis cyclist Remy Di Gregorio, with judicial officials saying two other people suspected of supplying the Frenchman with banned substances were also arrested — one along with the rider in Bourg-en-Bresse, and another in Marseille.
The officials requested anonymity because they were not authorized to speak publicly as the investigation is ongoing.
Cycling's premier showcase event has long been dogged by doping scandals.
Two-time winner Alberto Contador of Spain is sitting out this year to serve a doping ban from the 2010 race, while seven-time Tour champion Lance Armstrong has been charged with participating in a vast conspiracy by the U.S. Anti-Doping Agency. The American has declared his innocence and is asking a federal court to block USADA's case.
Di Gregorio's arrest comes after an investigation that began last June and is led by the French police agency responsible for doping investigations, OCLAESP, and Marseille police.
"(The police) have followed Remy's actions for a good while," Cofidis manager Yvon Sanquer said at a news conference. "If I had ever been aware or anyone else had been aware, Remy's time with the team would have been over the very moment when we learned of it."
Sanquer, who took up his post two days before the start of the race, said he found out about the arrest from police just before the team went on a training ride in the morning.
Sanquer said Di Gregorio's teammates reacted with a mix of "anger and devastation ... when I explained the situation to them, it was painful for them. There were tears."
The 26-year-old Di Gregorio was in 35th place after Monday's ninth stage. The Marseille native turned pro in 2005 with French team Francaise des Jeux, and was once considered one of the most promising young French riders.
When the investigation began, Di Gregorio was riding for Astana. He won one stage in the 2011 Paris-Nice race with the Kazahk team. This season, he has had one stage win, in the Spanish Tour of Asturias in April.
Sanquer said he believed Di Gregorio, who recently became a father, "didn't understand the breadth of what he was doing and the seriousness of what he could be doing" if the accusations turn out to be true.
"Cycling is about beautiful moments, and there also very difficult ones. This is one," Sanquer said. "There are other things — sickness, injury ... it's part of a series of things that riders have to get through."
In the 2008 Tour de France, Cofidis pulled out of the race following Italian rider Cristian Moreni's positive test for testosterone.
In 2004, French police arrested then-Cofidis riders David Millar of Britain and Cedric Vasseur of France in another doping investigation involving the team and seized male hormones, EPO and amphetamines.
Another former Cofidis rider, Phillipe Gaumont, accused several of his teammates and the team doctor at the time of wide-spread doping.
AP Sports Writer Samuel Petrequin and Associated Press Writer Jamey Keaten in Saint-Albain, France, contributed to this report.