| 1 | Nathan Haas (Aus) Genesys Wealth Advisers | 4:08:35 |
| 2 | Taiji Nishitani (Jpn) Aisan Racing Team | |
| 3 | Junya Sano (Jpn) d'Angelo & Antenucci - Nippo | |
| 4 | Damiano Cunego (Ita) Lampre - ISD | |
| 5 | Yusuke Hatanaka (Jpn) Shimano Racing Team | |
| 6 | Manuele Mori (Ita) Lampre - ISD | 0:00:02 |
| 7 | Damiano Caruso (Ita) Liquigas-Cannondale | |
| 8 | Miyataka Shimizu (Jpn) Bridgestone Anchor | 0:00:04 |
| 9 | Cristiano Salerno (Ita) Liquigas-Cannondale | 0:00:07 |
| 10 | Ivan Basso (Ita) Liquigas-Cannondale | 0:00:09 |
| 11 | Yukiya Arashiro (Jpn) Team Europcar | |
| 12 | Takashi Miyazawa (Jpn) Farnese Vini - Neri Sottoli | 0:00:30 |
| 13 | Ryota Nishizono (Jpn) Shimano Racing Team | |
| 14 | Shinichi Fukushima (Jpn) Terengganu Cycling Team | |
| 15 | Yukihiro Doi (Jpn) Skil - Shimano | |
| 16 | Vincenzo Garofolo (Ita) Matrix Powertag | |
| 17 | Masahiro Shinagawa (Jpn) Aisan Racing Team | |
| 18 | Gustav Larsson (Swe) Saxo Bank Sungard | |
| 19 | Andrey Mizurov (Kaz) Pro Team Astana | |
| 20 | Alexandre Shushemoin (Kaz) Pro Team Astana | |
| 21 | Makoto Nakamura (Jpn) Utsunomiya Blitzen | |
| 22 | Nic Hamlton (Can) Jelly Belly p/b Kenda | 0:00:47 |
| 23 | Masaru Fukuhara (Jpn) Bridgestone Anchor | 0:00:52 |
| 24 | Rafal Majka (Pol) Saxo Bank Sungard | 0:01:33 |
| 25 | Kenichi Suzuki (Jpn) Aisan Racing Team | 0:02:27 |
| 26 | Yuzuru Suzuki (Jpn) Shimano Racing Team | 0:03:33 |
| 27 | Mariusz Wiesiak (Pol) Matrix Powertag | 0:04:37 |
| 28 | Josep Jufre Pou (Spa) Pro Team Astana | |
| 29 | Henry Frusto (Ita) d'Angelo & Antenucci - Nippo | |
| 30 | Steele Von Hoff (Aus) Genesys Wealth Advisers | |
| 31 | Kazuo Inoue (Jpn) Bridgestone Anchor | |
| 32 | Tomoya Kano (Jpn) Bridgestone Anchor | |
| 33 | Shinri Suzuki (Jpn) Shimano Racing Team | 0:06:43 |
| 34 | Kazuki Aoyanagi (Jpn) Shimano Racing Team | 0:07:07 |
| 35 | Ryohei Komori (Jpn) d'Angelo & Antenucci - Nippo | 0:07:11 |
| 36 | Yoshimasa Hirose (Jpn) Utsunomiya Blitzen | 0:09:29 |
| 37 | Akira Kakinuma (Jpn) Utsunomiya Blitzen | |
| 38 | Kazuyuki Manabe (Jpn) Matrix Powertag | |
| 39 | Yoshiyuki Shimizu (Jpn) Bridgestone Anchor | |
| 40 | Ran Margaliot (Isr) Saxo Bank Sungard | |
| 41 | Daisei Nagara (Jpn) Matrix Powertag | |
| 42 | Tomohiro Hayakawa (Jpn) Aisan Racing Team | |
