Michel Boyon, president of the Council for Prevention of Drug Use (CPLD), said in a press release that the first results of anti-doping tests taken during this year's Tour revealed the shock results.
"Analyses of samples at the national laboratory at Chatenay-Malabray revealed the presence of doping products in 45 percent of the urine tests," he said.
The International Cycling Union (UCI) angrily dismissed the results, saying it stood by its own doping tests during the Tour which came back negative for banned substances.
Boyon said 96 tests had been performed on 71 riders during the race. Four were tested for each of the first 15 stages and 12 were made during the 16th to 20th stages.
He said 28 tests were positive for cortico-steroids, which reduce fatigue, and 10 tests were positive for stimulants salbutamol and terbutaline, which aid breathing. He said five tests revealed the presence of both drugs.
But the UCI said 26 of the 28 had medical clearance to use cortico-steroids and they were still investigating the two remaining cases.
It also dimissed the 10 cases involving salbutamol and terbutaline.
"We are following the rules of the IOC. Maybe these people don't know the rules," said UCI spokesman Enrico Carpani. "They (CPLD) have created confusion."
The UCI said of nine tests that found traces of salbutamol, all were within or below International Olympic Committee approved limits.
Medical reasons
The one positive result for terbutaline was prescribed for the rider and validated in his medical passport, said the union.
Boyon did not reveal the names of the riders who had tested positive and admitted some could have had medical reasons for using the drugs.
The drug agency said it had used French government standards in compiling its results.
Three riders were sent home before the start of the Tour after blood tests proved they had illegal levels of hematacrite - which suggests use of the banned hormone erythropoietin (EPO).
Tour de France officials were not immediately available on Tuesday for comment on the CPLD report.
But the French Ministry of Sport issued a statement saying that the figures confirmed "the necessity to continue the fight against doping."
The ministry said in its statement that sports minister Marie-George Buffet was concerned with the number of high-level sportsmen who use "therapeutic medicine" to help them succeed in sport.
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