The Manchester United man has a knee injury that is expected to rule him out of action until the end of Novemnber.
Ryo Miyaichi is another of Japan’s English Premier League stars absent but the Arsenal winger, on loan to Wigan Athletic, has been struggling to find playing time in the north-west of England and will not feature.
Other stars such as Keisuke Honda of CSKA Moscow and Inter Milan defender Yuto Nagatomo are fit and raring to go.
Coach Alberto Zaccheroni believes that the Samurai Blue, five points clear at the top of Group B with ten points from four games, will manage just fine in Muscat.
“Kagawa and Honda have been regular features in my squads but they haven’t always been available because of injuries,” the Italian said.
“But the players who have come in to deputise have all performed well. Kagawa is missing but I’m confident whoever plays will do a job.”
Goalkeepers - Eiji Kawashima (Standard Liege), Shusaku Nishikawa (Sanfrecce Hiroshima), Shuichi Gonda (FC Tokyo)
Defenders – Yuichi Komano (Jubilo Iwata), Yasuyuki Konno (Gamba Osaka), Yuzo Kurihara (Yokohama F-Marinos), Masahiko Inoha (Vissel Kobe), Yuto Nagatomo (Inter Milan), Atsuto Uchida (Schalke), Maya Yoshida (Southampton), Hiroki Sakai (Hannover)
Midfielders – Yasuhito Endo (Gamba Osaka), Kengo Nakamura (Kawasaki Frontale), Makoto Hasebe (Wolfsburg), Hajime Hosogai (Bayer Leverkusen), Keisuke Honda (CSKA Moscow), Hideto Takahashi (FC Tokyo)
Forwards – Ryoichi Maeda (Jubilo Iwata), Shinji Okazaki (Stuttgart), Mike Havenaar (Vitesse Arnhem), Takashi Inui (Eintracht Frankfurt), Hiroshi Kiyotake (Nuremberg), Takashi Usami (Hoffenheim)