(All Session Laps)
| Pos. | No. | Drivers | Car | Entrant | All Best | Q Time | FL Time | P1 Time |
| 1st | 38 | Tachikawa / Takagi | Lexus SC430 (UZZ40) | Toyota Team Cerumo | 1:55.302 | 1:56.5120 | 1:58.0670 | 1:55.3020 |
| 2nd | 32 | Duval / Carbone | Honda NSX (LA-NA2) | Nakajima Racing | 1:55.402 | 1:55.8170 | | 1:55.4020 |
| 3rd | 12 | Tréluyer / Hoshino / Dufour | Nissan Fairlady Z (Z33) | Team Impul | 1:55.981 | 1:55.9810 | | 1:56.4950 |
| 4th | 3 | Philippe / Yanagida | Nissan Fairlady Z (Z33) | Hasemi Motorsport | 1:56.043 | 1:56.2000 | | 1:56.0430 |
| 5th | 25 | Tsuchiya / Orido | Lexus SC430 (UZZ40) | Toyota Team Tsuchiya | 1:56.045 | 1:56.2640 | | 1:56.0450 |
| 6th | 18 | Michigami / Kogure | Honda NSX (LA-NA2) | Dome Racing Team | 1:56.129 | 1:56.1410 | | 1:56.1290 |
| 7th | 17 | Kaneishi / Kaneishi / Izawa | Honda NSX (LA-NA2) | Rolling Stone Real Racing | 1:56.262 | 1:56.2940 | | 1:56.2620 |
| 8th | 8 | Itou / Firman / Ide | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:56.284 | 1:56.2840 | | 1:57.0030 |
| 9th | 6 | Kataoka / Wirdheim | Lexus SC430 (UZZ40) | Forum Eng. Toyota Team Le Mans | 1:56.379 | 1:56.3790 | | 1:57.1570 |
| 10th | 100 | Hosokawa / Schwager | Honda NSX (LA-NA2) | Team Kunimitsu | 1:56.405 | 1:56.4050 | | 1:56.4170 |
| 11th | 22 | Krumm / Matsuda | Nissan Fairlady Z (Z33) | Nismo | 1:56.789 | 1:57.0840 | 1:58.1400 | 1:56.7890 |
| 12th | 1 | Wakisaka / Jarvis / Lotterer | Lexus SC430 (UZZ40) | Toyota Team Tom's | 1:56.867 | 1:56.8670 | | 1:57.6010 |
| 13th | 35 | Hattori / Dumbreck / Quintarelli | Lexus SC430 (UZZ40) | Toyota Team Kraft | 1:56.896 | 1:56.8960 | | 1:59.1200 |
| 14th | 23 | Motoyama / Yasuda / Lyons | Nissan Fairlady Z (Z33) | Nismo | 1:56.910 | 1:56.9100 | 1:57.9980 | 1:56.9530 |
| 15th | 24 | de Oliveira / Ara | Nissan Fairlady Z (Z33) | Kondo Racing | 1:57.565 | 1:57.5650 | | 1:58.0590 |
| 16th | 39 | Couto / Hiranaka | Lexus SC430 (UZZ40) | Toyota Team Sard | 1:57.903 | 1:57.9030 | | 1:58.0180 |
| 17th | 43 | Nitta / Takagi | ASL Garaiya | Autobacs Racing Team Aguri | 2:06.102 | 2:06.6960 | 2:08.6940 | 2:06.1020 |
| 18th | 62 | Shibahara / Kurosawa | Vemac RD408R | Willcom R&D Sport | 2:07.005 | 2:07.0050 | 2:09.3970 | 2:07.7510 |
| 19th | 13 | Kageyama / Fujii | Nissan Fairlady Z (Z33) | Endless Sports | 2:07.021 | 2:07.0210 | | 2:09.0650 |
| 20th | 2 | Takahashi / Katou / Yoshimoto | Shiden MC/RT-16 | Cars Tokai Dream28 | 2:07.154 | 2:07.1540 | 2:07.5150 | 2:07.6780 |
| 21st | 101 | Oshima / Ishiura | Toyota MR-S (GH-ZZW30) | Apr | 2:07.180 | 2:07.1800 | | 2:07.6970 |
| 22nd | 77 | Yamano / Aoki / Kobayashi | Subaru Impreza (GD) | Cusco Racing | 2:07.330 | 2:07.3300 | | 2:08.8380 |
| 23rd | 31 | Mineo / Sakamoto | Toyota MR-S (GH-ZZW30) | Apr | 2:07.332 | 2:07.3320 | | 2:08.7630 |
| 24th | 26 | Taniguchi / Farnbacher / Nishizawa | Porsche 996 GT3-RS | Team Taisan With Nishizawa | 2:07.597 | 2:07.5970 | | 2:07.8000 |
| 25th | 5 | Tamanaka / Takeuchi / Sawa | Vemac RD320R | Team Mach | 2:07.674 | 2:07.6740 | | 2:08.4820 |
| 26th | 7 | Iiri / Orime / Yamano | Mazda RX-7 (FD3S) | RE Amemiya Racing | 2:07.722 | 2:07.7220 | | 2:08.5140 |
| 27th | 46 | Sasaki / Yokomizo | Nissan Fairlady Z (Z33) | Mola | 2:07.748 | 2:07.7910 | | 2:07.7480 |
| 28th | 4 | Tanaka / Yamazaki / Watanabe | Vemac RD350R | Ebbro Team Nova | 2:07.806 | 2:07.8880 | | 2:07.8060 |
| 29th | 55 | Ikeda / Bamba / Fukuyama | Ford GT (DHG-replica) | Dhg Racing | 2:07.903 | 2:07.9030 | | 2:08.7570 |
| 30th | 11 | Ueda / Suga / Matsuda | Ferrari 360 Modena (GF-F360) | Jim Gainer | 2:08.558 | 2:08.5580 | | 2:09.1210 |
| 31st | 19 | Iida / Sekiguchi | Toyota Celica (ZZT231) | Racing Project Bandoh | 2:08.764 | 2:08.7640 | | 2:09.5990 |
| 32nd | 110 | Kurosawa / Mitsusada | Porsche 986 Boxster | Arktech Motorsports | 2:08.770 | 2:08.7700 | | 2:09.5630 |
| 33rd | 47 | Wakisaka / Mitsuyama | Nissan Fairlady Z (Z33) | Mola | 2:08.811 | 2:08.8110 | | 2:09.5140 |
| 34th | 33 | Kinoshita / Sakamoto | Porsche 996 GT3-R | Hankook Ktr | 2:09.258 | 2:09.2580 | | 2:10.0440 |
| 35th | 333 | Uematsu / Sakaguchi / Inoue | Porsche 996 GT3-RSR | Mario Racing With Ishimatsu | 2:09.374 | 2:09.3740 | | 2:09.7410 |
| 36th | 111 | Kikuchi / Jounai / Tsubobayashi | Porsche 986 Boxster | Arktech Motorsports | 2:09.375 | 2:09.3750 | | 2:10.2120 |
| 37th | 666 | Suhou / Yamashita / Shimoyama | Vemac RD320R | Avanzza x Bomex | 2:09.458 | 2:09.4580 | | 2:13.8420 |
| 38th | 9 | Tanaka / Tsutsui / Nakajima | Mosler MT900R (OOX) | A&S Racing | 2:10.237 | 2:10.2370 | | 2:12.3140 |
| 39th | 70 | Ishibashi / Koizumi / "Oyaji" | Porsche 996 GT3-RS | Team Gaikokuya | 2:12.579 | 2:12.5790 | | 2:13.7310 |
| 40th | 67 | Kurosawa / Wada / Furuya | Lamborghini Gallardo RG-3 | JLOC | 2:14.830 | 2:15.8810 | | 2:14.8300 |
Entered cars that did not arrive:
| No. | Drivers | Car | Entrant |
| 66 | Furuya / Kurihara / Yogou | Lamborghini Gallardo RG-3 | JLOC |
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