"After giving it a lot of thought, I have decided, after agreeing with the national coach and my Deceuninck-Quickstep team, not to make myself available for selection for the upcoming Tokyo Olympics," Alaphilippe wrote on Twitter.
"It is a personal, well-considered decision."
Alaphilippe came back from a crash to finish fourth in the Rio Olympics road race in 2016 after going in as one of the main favourites to break France's 60-year drought in the men's event.
Now, the 28-year-old, who won La Flèche Wallonne and a stage in Tirreno-Adriatico will likely target the World Championships in Flanders.
"End-of-season objectives have been defined and in this sense choices must be made," Alaphilippe continued. "I would be very proud to wear the France team jersey for the next world championships."
Alaphilippe is also due to form one of the cornerstones of Deceuninck-Quickstep's Tour de France team, and the race ends just days before the men's road race in Tokyo, and he and partner Marion Rousse are reportedly expecting their first child in June.
"Of course, I wish the best for the team that will be lined up on this occasion," he concluded, wishing luck to his French national team.
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