Scarlets centre Jason Williams led the way with two tries and a conversion as the Welsh players got some valuable game time ahead of next months' FIRA/AER Under 18 Championship in France.
The Japanese tourists, who left Tokyo in the immediate aftermath of the earthquake and tsunami, started their tour well with two wins in Scotland. They beat a Glasgow Hawks development side 22-5 before outscoring the Scottish Under 18s by four tries to two in a 20-13 victory.
Their first game in Wales was against a Dragons Academy team, when they went down 31-22 at Rodney Parade, and they were once again overcome in a free-flowing game at Pandy Park.
But while they were beaten, the tourists managed to score five tries themselves and in full back Yoshikazu Sujita they had the outstanding player on the field.
Back rower Hayato Nishiuchi was another player to shine and he had a tremendous battle with one of Wales' star performers, openside flanker Dan Thomas.
Thomas claimed one of the home tries, while Japanese No8 Ryota Suginaga outdid him by crossing the home line twice.
Welsh wing Ryan Evans also scored a brace of tries and the home scoring was completed by a try from Aaron Evans and two conversions and a penalty by outside half Rhys Pratchell.
Wales President's XV: Dion Jones; Aron Evans, Ryan Edwards Evans, Jordan Williams, Ryan Evans; Rhys Patchell, Josh Davies; Nicky Smith, Evan Yardley, Daniel Suter, Llewellyn Jones, Jack Jones (captain), Sion Bennett, Daniel Thomas, Lewis Young
Replacements: Elliot Dee, Calum Lewis, Bradley Thyer, Rhodri Hughes, Ieuan Jones, Alex Schwrtz, Ben Roberts, Owen Jenkins