| # | Group A | MP | W | D | L | G | GD | Pts | Form |
|---|---|---|---|---|---|---|---|---|---|
| 1. | Garudayaksa | 13 | 5 | 6 | 2 | 15:8 | 7 | 21 | |
| 2. | Adhyaksa | 13 | 5 | 5 | 3 | 16:15 | 1 | 20 | |
| 3. | Persikad Depok | 14 | 4 | 4 | 6 | 19:25 | -6 | 16 | |
| 4. | Persiraja Aceh | 13 | 3 | 5 | 5 | 15:17 | -2 | 14 | |
| 5. | Bekasi City | 13 | 3 | 5 | 5 | 15:17 | -2 | 14 | |
| 6. | PSPS Riau | 14 | 3 | 5 | 6 | 30:33 | -3 | 14 | |
| 7. | PSMS Medan | 14 | 2 | 5 | 7 | 16:21 | -5 | 11 | |
| 8. | Sumsel United | 13 | 3 | 2 | 8 | 14:20 | -6 | 11 | |
| 9. | Persekat | 14 | 3 | 1 | 10 | 10:28 | -18 | 10 | |
| 10. | Sriwijaya | 14 | 0 | 2 | 12 | 8:55 | -47 | 2 | |
| # | Group B | MP | W | D | L | G | GD | Pts | Form |
| 1. | Barito Putera | 13 | 7 | 3 | 3 | 14:8 | 6 | 24 | |
| 2. | Deltras Sidoarjo | 13 | 7 | 1 | 5 | 19:16 | 3 | 22 | |
| 3. | Persipura Jayapura | 13 | 6 | 3 | 4 | 18:11 | 7 | 21 | |
| 4. | PSS Sleman | 13 | 5 | 5 | 3 | 21:12 | 9 | 20 | |
| 5. | Tornado Pekanbaru | 13 | 6 | 2 | 5 | 18:14 | 4 | 20 | |
| 6. | Persela Lamongan | 14 | 5 | 5 | 4 | 14:15 | -1 | 20 | |
| 7. | Persiku Kudus | 14 | 3 | 3 | 8 | 18:20 | -2 | 12 | |
| 8. | PSIS Semarang | 14 | 2 | 4 | 8 | 10:25 | -15 | 10 | |
| 9. | Balikpapan | 14 | 1 | 4 | 9 | 11:25 | -14 | 7 | |
| 10. | Persipal BU | 14 | 0 | 1 | 13 | 9:59 | -50 | 1 |