| # | Group A | MP | W | D | L | G | GD | Pts | Form |
|---|---|---|---|---|---|---|---|---|---|
| 1. | Vissel Kobe | 6 | 5 | 1 | 0 | 15:3 | 12 | 16 | |
| 2. | Omiya Ardija | 6 | 4 | 2 | 0 | 5:1 | 4 | 14 | |
| 3. | Kofu | 6 | 2 | 2 | 2 | 3:4 | -1 | 8 | |
| 4. | Shonan Bellmare | 6 | 2 | 1 | 3 | 4:6 | -2 | 7 | |
| 5. | Iwata | 6 | 1 | 2 | 3 | 4:7 | -3 | 5 | |
| 6. | Kashima Antlers | 6 | 1 | 1 | 4 | 8:12 | -4 | 4 | |
| 7. | Nagoya Grampus | 6 | 1 | 1 | 4 | 4:10 | -6 | 4 | |
| # | Group B | MP | W | D | L | G | GD | Pts | Form |
| 1. | Yokohama F. Marinos | 6 | 3 | 2 | 1 | 7:5 | 2 | 11 | |
| 2. | Avispa Fukuoka | 6 | 2 | 3 | 1 | 9:7 | 2 | 9 | |
| 3. | Kawasaki Frontale | 6 | 2 | 2 | 2 | 9:5 | 4 | 8 | |
| 4. | Kashiwa Reysol | 6 | 2 | 2 | 2 | 9:8 | 1 | 8 | |
| 5. | Vegalta Sendai | 6 | 2 | 2 | 2 | 4:5 | -1 | 8 | |
| 6. | Albirex Niigata | 6 | 2 | 1 | 3 | 6:12 | -6 | 7 | |
| 7. | Sagan Tosu | 6 | 0 | 4 | 2 | 4:6 | -2 | 4 |