(Grid Positions)
| Grid | No. | Drivers | Car | Entrant | Q Time |
| 1st | 19 | Kazuyoshi Hoshino | Cerumo 89Ge Mugen (Lola T88/50) | Cabin Racing Team With Impul | 1:21.8120 |
| 2nd | 24 | Emanuele Pirro | MCS 9 Mugen (Reynard 89DGC) | Kawai Steel Racing Team Le Mans | 1:22.3350 |
| 3rd | 15 | Hideki Okada | March 89GC Mugen | Leyton House Racing Team | 1:22.5770 |
| 4th | 16 | Masanori Sekiya | March 89GC Mugen | Leyton House Racing Team | 1:22.7510 |
| 5th | 25 | Geoff Lees | MCS 9 Mugen (Reynard 89DGC) | Kawai Steel Racing Team Le Mans | 1:22.8950 |
| 6th | 7 | Kunimitsu Takahashi | Cerumo 89Ge Mugen (Lola T88/50) | Advan Sports Nova | 1:23.0070 |
| 7th | 26 | Takao Wada | Mad House F4 Mugen (Lola T88/50) | Advan Sport Pal | 1:23.2670 |
| 8th | 8 | Keiji Matsumoto | MCS 9 Mugen (Lola T88/50) | Meiju Racing Team | 1:23.9380 |
| 9th | 60 | Takashi Yorino | Cerumo 89Ge Mazda (Lola T88/50) | Itoham Racing Team | 1:24.4690 |
| 10th | 6 | Eje Elgh | R&D 88Q Mazda (Lola T88/40) | Sundai Spilit Team | 1:24.6380 |
| 11th | 17 | Tetsuya Oota | MCS 8 Mugen (Lola T87/50) | Checker Motors & Noji | 1:24.7310 |
| 12th | 31 | Katsunori Iketani | MCS 8 Ford (Lola T87/50) | Super Cad With Checker | 1:25.3780 |
| 13th | 28 | Kazuo Mogi | MCS 9 Ford (Lola T88/50) | Fet With Zoom Racing | 1:25.7690 |
| 14th | 33 | Masatomo Shimizu | Mad House Ford (Lola T86/50) | Shimizu Racing | 1:26.5260 |
| 15th | 2 | Yojiro Terada | R&D 89Q Mazda (March 88GC) | Artnature Racing Team | 1:26.9810 |
| 16th | 14 | Masahiro Kimoto | MCS 7 Ford (March 86B) | Hermanos Racing | 1:30.0980 |
| 17th | 46 | Fumio Mutou | MCS 7 Ford (March 86B) | TTS Racing | 1:32.2400 |
| 18th | 27 | Kaneyuki Okamoto | Okamoto 85SC Ford (March 88GC) | Okamoto Racing | 1:35.9910 |
Entered cars that did not arrive:
| No. | Drivers | Car | Entrant |
| 3 | Taku Akaike | Cerumo 89Ge Mugen | Team Taku |
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