It had been reported the 23-year-old would be selected as one of Japan’s three over-age players for their three group games in the UK, beginning at the end of July.
However, the prospective United new-boy has been omitted, meaning his summer break began after Tuesday’s World Cup qualifying draw with Australia.
Japanese FA technical director Hiromi Hara said: "Kagawa is one of the leading members of the Japan national senior team and he is almost certainly going to join one of the biggest clubs in the world.
"We came to the conclusion that not giving him enough rest is not good for his future nor our final World Cup qualifiers.
"I talked to Kagawa directly and told him he would not be chosen. We have other talented forward players and I hope they will make their presence felt."
Kagawa will complete his move to United from Borussia Dortmund if he passes a medical and obtains a work permit.
His first action for the Reds could be on the pre-season tour of South Africa in mid-July, though the travelling party will be announced nearer the time.