Minamino joined Southampton at the end of the January transfer window, and impressed during his time on south coast. Saints boss Ralph Hasenhuttl has admitted that he would like to make him a permanent addition to his squad.
Following Hasenhuttl's admission just days ago that he would be interested in making him a permanent addition, Minamino has withdrawn from his duties with Japan.
A brief statement from the Japanese Football Association read: "Takumi Minamino will be leaving due to club circumstances."
Minamino started in the 1-0 friendly win over Serbia on Friday, but that will be his final appearance with Japan this summer.
He will miss Tuesday's World Cup qualifying clash against Kyrgyzstan as a result.