The Manchester United ace was rested by Blue Samurai boss Alberto Zaccheroni after slightly injuring his back but the player himself feels he should be right to face Wigan Athletic at Old Trafford in the Premier League on Saturday.
"I felt a twinge in the back during practice when I was on the ball. I had some treatment but didn't want to risk causing the team trouble by playing," Kagawa told the Kyodo news agency.
"Obviously it's a shame I wasn't able to play... It's not that serious and I don't think it will keep me out for long."
Japan sits on top of the Group B table in Asian qualifying after four matches, eight points ahead of Australia who meet Jordan in their third fixture later on Tuesday.