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| # | Team | P | W | D | L | F | A | GD | PTS |
|---|---|---|---|---|---|---|---|---|---|
| 1 |  Mito Hollyhock | 28 | 15 | 8 | 5 | 44 | 27 | 17 | 53 |
| 2 |  JEF United Chiba | 28 | 15 | 6 | 7 | 39 | 25 | 14 | 51 |
| 3 |  V-Varen Nagasaki | 28 | 14 | 9 | 5 | 46 | 38 | 8 | 51 |
| 4 |  Tokushima Vortis | 28 | 13 | 9 | 6 | 28 | 15 | 13 | 48 |
| 5 |  Omiya Ardija | 28 | 13 | 8 | 7 | 38 | 23 | 15 | 47 |
| 6 |  Vegalta Sendai | 28 | 12 | 11 | 5 | 32 | 26 | 6 | 47 |
| 7 |  Jubilo Iwata | 28 | 13 | 6 | 9 | 43 | 36 | 7 | 45 |
| 8 |  Imabari FC | 28 | 11 | 10 | 7 | 35 | 29 | 6 | 43 |
| 9 |  Sagan Tosu | 28 | 12 | 7 | 9 | 31 | 29 | 2 | 43 |
| 10 |  Hokkaido Consadole Sapporo | 28 | 12 | 4 | 12 | 35 | 44 | -9 | 40 |
| 11 |  Ventforet Kofu | 28 | 10 | 8 | 10 | 29 | 27 | 2 | 38 |
| 12 |  Iwaki FC | 28 | 9 | 9 | 10 | 39 | 36 | 3 | 36 |
| 13 |  Montedio Yamagata | 28 | 9 | 5 | 14 | 39 | 41 | -2 | 32 |
| 14 |  Fujieda MYFC | 28 | 8 | 8 | 12 | 34 | 37 | -3 | 32 |
| 15 |  Blaublitz Akita | 28 | 9 | 5 | 14 | 36 | 46 | -10 | 32 |
| 16 |  Roasso Kumamoto | 28 | 8 | 6 | 14 | 33 | 42 | -9 | 30 |
| 17 |  Oita Trinita | 28 | 6 | 11 | 11 | 22 | 32 | -10 | 29 |
| 18 |  Kataller Toyama | 28 | 5 | 8 | 15 | 22 | 36 | -14 | 23 |
| 19 |  Renofa Yamaguchi | 28 | 3 | 13 | 12 | 25 | 36 | -11 | 22 |
| 20 |  Ehime FC | 28 | 2 | 11 | 15 | 25 | 50 | -25 | 17 |