| # | Rider | Team | Time | Gap |
|---|---|---|---|---|
| 1 | Daniel Martin | Garmin-Transitions | 04:02:28 | |
| 2 | Peter Mcdonald | Drapac - Porsche Cycling | + 57 | + 57 |
| 3 | Yusuke Hatanaka | Shimano Racing Team | + 57 | + 57 |
| 4 | Taiji Nishitani | Aisan Racing Team | + 57 | + 57 |
| 5 | Shinri Suzuki | Shimano Racing Team | + 57 | + 57 |
| 6 | Takashi Miyazawa | Team Nippo | + 57 | + 57 |
| 7 | Johannes Fröhlinger | Team Milram | + 57 | + 57 |
| 8 | Anders Lund | Team Saxo Bank | + 57 | + 57 |
| 9 | Yukiya Arashiro | BBOX Bouygues Telecom | + 57 | + 57 |
| 10 | Luca Mazzanti | Team Katusha | + 57 | + 57 |
| 11 | Thomas Peterson | Garmin-Transitions | + 01:01 | + 01:01 |
| 12 | Shinichi Fukushima | Geumsan Ginseng Asia | + 01:01 | + 01:01 |
| 13 | Masahiro Shinagawa | Aisan Racing Team | + 01:03 | + 01:03 |
| 14 | Junya Sano | Team Nippo | + 01:10 | + 01:10 |
| 15 | Kenji Itami | Team Bridgestone - Anchor | + 01:56 | + 01:56 |
| 16 | Yukihiro Doi | + 01:58 | + 01:58 | |
| 17 | Timothy Duggan | Garmin-Transitions | + 02:00 | + 02:00 |
| 18 | Kazuo Inoue | Team Nippo | + 02:15 | + 02:15 |
| 19 | Jure Golcer | De Rosa - Stac Plastic | + 02:20 | + 02:20 |
| 20 | Cristiano Salerno | De Rosa - Stac Plastic | + 02:24 | + 02:24 |
| 21 | Takeshi Igarashi | Geumsan Ginseng Asia | + 03:04 | + 03:04 |
| 22 | Masaru Fukuhara | Team Bridgestone - Anchor | + 03:07 | + 03:07 |
| 23 | Jumpei Murakami | Shimano Racing Team | + 03:07 | + 03:07 |
| 24 | Takumi Beppu | Aisan Racing Team | + 03:09 | + 03:09 |
| 25 | Hayato Yoshida | + 03:09 | + 03:09 | |
| 26 | Kenichi Suzuki | Aisan Racing Team | + 03:22 | + 03:22 |
| 27 | Ryota Nishizono | + 03:40 | + 03:40 | |
| 28 | Wim de Vocht | Team Milram | + 05:59 | + 05:59 |
| 29 | Thomas Palmer | Drapac - Porsche Cycling | + 05:59 | + 05:59 |
| 30 | Joseph Lewis | Drapac - Porsche Cycling | + 05:59 | + 05:59 |
| 31 | Perrig Quemeneur | BBOX Bouygues Telecom | + 05:59 | + 05:59 |
| 32 | Gustav Larsson | Team Saxo Bank | + 05:59 | + 05:59 |
| 33 | Ryohei Komori | + 05:59 | + 05:59 | |
| 34 | Yuzuru Suzuki | Shimano Racing Team | + 05:59 | + 05:59 |
| 35 | Akira Kakinuma | Utsunomiya Blitzen | + 05:59 | + 05:59 |
| 36 | Tomoya Kano | Team Bridgestone - Anchor | + 05:59 | + 05:59 |
| 37 | Makoto Iijima | Team Bridgestone - Anchor | + 05:59 | + 05:59 |
| 38 | Masaaki Kikuchi | Team Nippo | + 08:57 | + 08:57 |
| 39 | Phuchong Sai-udomsin | Geumsan Ginseng Asia | + 09:17 | + 09:17 |
| 40 | André Steensen | Team Saxo Bank | + 10:04 | + 10:04 |
| 41 | Yoshimitsu Hiratsuka | Shimano Racing Team | + 10:14 | + 10:14 |
| 42 | Makoto Nakamura | Utsunomiya Blitzen | + 12:09 | + 12:09 |