Kagawa to undergo surgery on foot
Kagawa broke his fifth metatarsal in his foot during his team's semi-final against South Korea this week and is expected to miss the rest of the season.
"He is on his way to Japan for surgery," the club said in a statement. "It was his wish and the club agreed. It is not yet decided when he will return to Germany."
Dortmund said it was unlikely the player would return before the end of the season.
"There are variations in this injury but I do not know of any case that a player came back earlier than three months," said Dortmund coach Jurgen Klopp.
Kagawa, snapped up in the close season from Japan's second division for 350,000 euros, has been crucial in Dortmund's spectacular run this season with his team eight points clear at the top of the table.
The 21-year-old has scored eight league goals in his first season in Germany and his value is now estimated at around seven million euros.