The 23-year-old was expected to feature in the 2014 World Cup qualifier in Saitama but the former Borussia Dortmund star pulled out of the tie with a slight back strain.
However, Kagawa insisted it was a precautionary move, with Japan manager Alberto Zaccheroni unwilling to risk the Red Devils playmaker.
“I underwent treatment for as long as possible before the match and [Japan coach Alberto Zaccheroni] waited for me,” said Kagawa. “I felt a twinge and didn’t want to take the risk.
“It’s not a serious injury and I don’t think it will keep me out for long. I can walk without any problem but if I put strain on it still hurts.”
Zaccheroni added: “I waited until the afternoon to see how his condition was but there’s no way I can put a player on the pitch who is not at 100 per cent.”
Earlier this week, veteran United midfielder Paul Scholes heaped praise on Kagawa after the Japan international made an impressive start to his career in the English top flight following a £12m move to Old Trafford.
“All the new signings have settled in well. Shinji [Kagawa] has been with us since the start of pre-season so he’s had a good amount of time to settle in. He’s a top class player who did great in Germany and we’re lucky to have him,“ Scholes told United’s website.
“Shinji is just a clever footballer who gets into those great positions where it’s difficult for other teams to pick him up. He’s always on the move which makes it easier for the midfielders to find him.
“He really fits in with the way we play. It’s important that he links up well with the midfielders and centre forwards and he’s already shown he’s clever enough to do that. He’s very intelligent and someone we all enjoy playing with.”
MORE: Man United latest news
MORE: Arsenal latest news
MORE: Chelsea latest news
MORE: Liverpool latest news