The match comes as a warm-up to Sunday's non-cap international at Tokyo's National Stadium, and saw some of the fringe players from the recent Churchill Cup get amongst the points.
England found themselves up against resilient opponents in the opening half, and led by only one point at the interval, with the score at 11-10 to the visitors.
Captain and Sale Sharks back row Pete Anglesea scored one of the five tries on the day, while Bath centre Olly Barkley touched down twice for the team coached by Sale's Jim Mallinder and Steve Diamond.
New Leeds wing Phil Christophers also scored, as did his Tykes team-mate Dan Scarbrough, the fullback who has impressed in the England 'A' colours this season.
Barkley added three conversions and two penalties to make the result a formality, despite the Japan Select XV putting up a decent fight.
Montferrand wing Daisuke Ohata scored their only try of the match, with left-wing Toru Kurihara of the powerful Suntory club converting it and adding a penalty.
For the Japan Select XV:Try: OhataCon: KuriharaPen: Kurihara
For England:Tries: Barkley 2, Anglesea, Christophers, ScarbroughCons: Barkley 3Pens: Barkley 2
Japan Select XV: 15 M Tsutomu (Toshiba Fuchu), 14 D Ohata (Montferrand), 13 H Namba (Toyota Motor), 12 Y Motoki (Kobe Steel), 11 T Kurihara (Suntory), 10 K Hirose (Toyota Motor), 9 Y Sonoda (Kobe Steel), 8 Y Saito (Colomiers), 7 T Miuchi (NEC, captain), 6 T Ito (Kobe Steel), 5 A Parker (Toshiba Fuchu), 4 H Kiso (Yamaha Motor), 3 M Toyoyama (Toyota Motor), 2 M Amino (NEC), 1 S Hasegawa (Suntory).Replacements: 16 M Yamamoto (Toyota Motor), 17 H Matsuo (Toshiba Fuchu), 18 K Kubo (Yamaha Motor), 19 Y Watanabe (Toshiba Fuchu), 20 W Murata (Yamaha Motor), 21 R Parkinson (Sanix), 22 H Onozawa (Suntory).
England XV: 15 Michael Horak (London Irish), 14 Dan Scarbrough (Leeds Tykes), 13 Fraser Waters (London Wasps), 12 Ben Johnston (Saracens), 11 Phil Christophers (Leeds Tykes), 10 Olly Barkley (Bath), 9 Nick Walshe (Sale Sharks), 8 Pete Anglesea (Sale Sharks, captain), 7 Andy Hazell (Gloucester), 6 Paul Volley (London Wasps), 5 Alex Codling (Saracens), 4 Chris Jones (Sale Sharks), 3 Neil Hatley (London Irish), 2 Matt Cairns (Sale Sharks), 1 David Flatman (Bath).Replacements: 16 Andy Titterrell (Sale Sharks), 17 Andy Sheridan (Sale Sharks), 18 Will Green (London Wasps), 19 Alex Brown (Gloucester), 20 Dan Hyde (Leeds Tykes), 21 Henry Paul (Gloucester), 22 Martyn Wood (Bath).