The Japanese sports newspaper Sponichi reports that, at a press conference, the 33-year-old announced he is leaving the team due to a left-foot injury.
Wataru Endo had foot surgery in February and has been training on his own in the USA; the hope was that he would be ready to play in Japan's opening match against the Netherlands on Sunday.
That's not going to happen.
Ko Itakura of Ajax becomes the new team captain, and striker Shuto Machino of Mönchengladbach has been called up as Endo's replacement.
Sweden will face Japan in the final group-stage match on the night of June 26.
