Norio Sasaki took responsibility after Saki Kumagai, who scored the winning penalty in a shoot-out to stun the United States at Sunday's final in Frankfurt, apparently criticised the coach during a night out.
"It's because of my lack of supervision," Sasaki told Japanese media. "I deeply apologise to everyone who has been so supportive of 'Nadeshiko' Japan (the women's team)."
Local media reported that Kumagai's remarks about Sasaki and the team pecking order were made public, while the player, who has apologised on her own Twitter page, has been pulled from all scheduled television appearances in the wake of the gaffe.
Japan's Kyodo News agency reported Kumagai also allegedly showed racy photos of team mate Karina Maruyama while at dinner with college friends.
"I understand she has been holed up in hotel for a long time," Japan Football Association vice president Kuniya Daini told the Sankei Sports.
"But I will instruct those in charge at the clubs (the players belong to) not to allow such frivolous behaviour to continue."
Japan's "Nadeshiko," named after a frilly pink carnation symbolising beauty and stoicism, stunned the world with their astonishing run to the title in Germany.
They beat hosts and holders Germany in the quarter-finals, powerhouse Sweden in the semi-finals, before a cliff-hanging win over hot favourites the U.S. in the final.
Their remarkable victory, Asia's first football world title at any level, was hailed as a beacon of hope for the victims of Japan's deadly earthquake and tsunami in March.