(All Session Laps)
| Pos. | No. | Drivers | Car | Entrant | All Best | Q Time | FL Time |
| 1st | 16 | Masanori Sekiya | March 89GC Mugen | Leyton House Racing Team | 1:53.185 | 1:53.1850 | |
| 2nd | 25 | Geoff Lees | MCS 9 Mugen (Reynard 89DGC) | Kawai Steel Racing Team Le Mans | 1:54.418 | 1:54.4180 | 1:58.5120 |
| 3rd | 8 | Keiji Matsumoto | MCS 9 Mugen (Lola T88/50) | Meiju Racing Team | 1:54.590 | 1:54.5900 | |
| 4th | 15 | Hideki Okada | March 89GC Mugen | Leyton House Racing Team | 1:54.682 | 1:54.6820 | |
| 5th | 24 | Akihiko Nakaya | MCS 9 Mugen (Reynard 89DGC) | Kawai Steel Racing Team Le Mans | 1:54.696 | 1:54.6960 | |
| 6th | 19 | Kazuyoshi Hoshino | Cerumo 89Ge Mugen (Lola T88/50) | Cabin Racing Team With Impul | 1:55.064 | 1:55.0640 | |
| 7th | 7 | Kunimitsu Takahashi | Cerumo 89Ge Mugen (Lola T88/50) | Advan Sports Nova | 1:55.193 | 1:55.1930 | |
| 8th | 26 | Takao Wada | Mad House F4 Mugen (Lola T88/50) | Advan Sport Pal | 1:55.712 | 1:55.7120 | |
| 9th | 17 | Tetsuya Oota | MCS 8 Mugen (Lola T87/50) | Checker Motors & Noji | 1:56.523 | 1:56.5230 | |
| 10th | 28 | Kazuo Mogi | MCS 9 Ford (Lola T88/50) | Fet With Zoom Racing | 1:57.647 | 1:57.6470 | |
| 11th | 6 | Eje Elgh | R&D 88Q Mazda (Lola T88/40) | Sundai Spilit Team | 1:58.108 | 1:58.1080 | |
| 12th | 70 | Yoshimi Katayama | MCS 7 Mazda (March 86B) | Lenox Katayama Racing | 1:58.241 | 1:58.2410 | |
| 13th | 60 | Takashi Yorino | Cerumo 89Ge Mazda (Lola T88/50) | Itoham Racing Team | 1:58.404 | 1:58.4040 | |
| 14th | 2 | Yojiro Terada | R&D 89Q Mazda (March 88GC) | Artnature Racing Team | 2:01.816 | 2:01.8160 | |
| 15th | 14 | Masahiro Kimoto | MCS 7 Ford (March 86B) | Hermanos Racing | 2:04.346 | 2:04.3460 | |
| 16th | 5 | Masahiro Hasemi | MCS 9 Mugen (Lola T87/50) | Speed Star Wheel Racing Team | 2:29.283 | 2:29.2830 | |
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