| Lane/Order | TEAM | Seeding Time | Note | |
|---|---|---|---|---|
| 1 | LAHAD DATU | LAHAD DATU | 3:29.25 | q |
| 2 | KENINGAU | KENINGAU | 3:30.45 | q |
| 3 | TAWAU | TAWAU | 3:36.42 | Q |
| 4 | KOTA KINABALU | KOTA KINABALU | 3:33.86 | Q |
| 5 | KINABATANGAN | KINABATANGAN | 3:33.82 | Q |
| 6 | KALABAKAN | KALABAKAN | 3:26.35 | Q |
| 7 | SANDAKAN | SANDAKAN | 3:28.94 | Q |
| 8 | TONGOD | TONGOD | 3:46.77 | Q |