The decision follows a long-running dispute between the two bodies which stems from whether race organisers, including the Amaury Sport Organisation - which organises the Tour de France, or the sport's governing body, the UCI, should have the final say over who rides in their races.
Tour de France race director, Christian Prudhomme, said: “We have asked the FFC that the Tour be organised under their authority. The AFLD will therefore be in charge of the doping tests before and during the race."
The UCI branded the move "a bad decision for cycling" and judged it as "extremely regrettable for the sport and the unity of the cycling family".
In a statement to the press the UCI said: "It is not correct that ASO leaders, backed by the FFC, preferred to make the announcement during a press conference before warning the international federation beforehand. It constitutes additional evidence of the ASO's wish to no longer take into account the authority of the UCI concerning international cycling.”
The UCI also warned that "riders and teams by competing will expose themselves to sanctions through the fault of ASO leaders".
The Tour starts in Brest on July 5 and ends in Paris on July 27.
