Japan international Lee, who suffered with injury during pre-season after joining the club in January, is well down the pecking order at St Mary's and is yet to make a Premier League appearance.
Lee scored in Southampton's Capital One Cup win at Stevenage and, following another setback, regained his fitness in the U21 team and came on as a substitute in the FA Cup third-round defeat to Chelsea.
The 27-year-old heads back to FC Tokyo, subject to international clearance, ahead of their J-League 1 campaign which starts next month.
Lee is set to return to Southampton ahead of pre-season this summer.
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