Britain's Chris Froome won this year's race, which came under extra scrutiny as it was the first edition being staged since American Lance Armstrong admitted he had cheated his way to seven Tour de France titles from 1999 to 2005.
Team Sky's Froome, who had to face the media every day on the Tour, expressed his frustration during the race at being repeatedly questioned about doping in the sport.
Team Sky principal Dave Brailsford said during the three-week Tour that he was ready to give the World Anti-Doping Agency (WADA) all their team training data if that would help.
An International Cycling Union (UCI) statement issued on Tuesday said CADF took 622 blood and urine samples during the 100th edition of the Tour against 566 samples in 2012.
Working closely with the French Anti-Doping Agency (AFLD), CADF took 202 pre-competition samples and 419 during the race.
Reinforcing the strategy of targeted testing, 198 of the samples taken during this year's race were for the biological passport compared to 149 samples in 2012.
"This target testing strategy has been hugely facilitated by the excellent on-site cooperation between CADF and AFLD during the race," Rossi was quoted as saying on the UCI's official website (www.uci.ch).
The samples were analysed by the WADA-accredited laboratories of Chatenay-Malabry in France, Lausanne in Switzerland and Cologne in Germany.
The UCI and AFLD have also agreed to keep the samples taken for possible retrospective testing in the future.
(Writing by Ken Ferris; editing by Nick Mulvenney)
