"We have just learnt that one of our riders on the Tour de France may have tried to use banned substances to improve his performance," the French team said in a statement on Tuesday. "Remy Di Gregorio is therefore suspended provisionally."
Cofidis said the rider would be fired if proven guilty.
French investigative judge Annaick Le Goff opened the investigation on June 28, 2011, prosecutors said.
Cofidis rider Di Gregorio, who was on the Tour de France, was transferred to his hometown of Marseille after the gendarmerie raided the team's hotel early on Tuesday.
The source said Di Gregorio was being questioned with two other people after an investigation was opened last year into alleged trafficking of doping substances.
Di Gregorio, 26, who won a Paris-Nice stage last year, was regarded as the next great French climber when he started his professional career in 2005 but failed to live up to expectations.
In 2011, he joined Astana from FDJ before moving to Cofidis this season.
It was unclear whether Di Gregorio would be able to start Wednesday's 10th stage. Under French law, he can be detained for 48 hours.