Kagawa, who scored on his home debut for United against Fulham on Saturday, was one of the six forwards named in the 23-man squad on Thursday that will play a friendly against the United Arab Emirates next week before taking on Iraq on September 11 at Saitama.
However, Zaccheroni was not ready to gamble on the fitness of Miyaichi, who Wigan signed from Premier League rivals Arsenal on a season-long loan earlier this month.
"He (Miyaichi) doesn't have match fitness and you would have to go back to April for the last time he played 90 minutes," Zaccheroni was quoted as saying by the Kyodo news agency.
"His condition is not 100 per cent and if I had picked him it would have only made his situation more difficult," added the Italian.
Zaccheroni did not include Hisato Sato either even though the veteran striker tops the J-League scoring charts with 17 goals.
"I have been watching him (Sato) recently and he is playing well but the biggest reason I haven't picked him is that I don't want to make any major changes to the way of doing things with the team I have got," Zaccheroni said.
CSKA Moscow's Keisuke Honda returned to bolster the midfield for Japan who top Group B after beating Oman and Jordan and drawing with Australia.
The match assumes further significance as former Japan coach Zico is now in charge of Iraq.
"Zico is an experienced coach and he has a group of talented players. They looked good in the third round of qualifiers and have different qualities to ours," Zaccheroni said.
"We have to show the same mental approach we did for the games against Oman and Jordan," he added.
Goalkeepers: Eiji Kawashima (Standard Liege), Shusaku Nishikawa (Sanfrecce Hiroshima), Shuichi Gonda (FC Tokyo)
Defenders: Yuichi Komano (Jubilo Iwata), Daiki Iwamasa (Kashima Antlers), Masahiko Inoha (Vissel Kobe), Hiroki Mizumoto (Sanfrecce Hiroshima), Yuto Nagatomo (Inter Milan), Maya Yoshida (VVV Venlo), Gotoku Sakai (Stuttgart), 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), Shinji Kagawa (Manchester United), Hiroshi Kiyotake (Nuremberg), Genki Haraguchi (Urawa Reds)