| 38 | Hironori Takeuchi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:42.6880 |
| 64 | Tsugio Matsuda / Andre Lotterer | Honda NSX (LA-NA2) | Mobil1 Nakajima Racing | 1:42.7850 |
| 22 | Masami Kageyama / Richard Lyons | Nissan Skyline GT-R (BNR34) | NISMO | 1:43.1020 |
| 1 | Juichi Wakisaka / Akira Iida | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:43.1380 |
| 39 | Dominik Schwager / Manabu Orido | Toyota Supra (JZA80) | Toyota Team SARD | 1:43.4870 |
| 23 | Satoshi Motoyama / Michael Krumm | Nissan Skyline GT-R (BNR34) | NISMO | 1:43.5610 |
| 12 | Benoit Tréluyer / Yuuji Ide | Nissan Skyline GT-R (BNR34) | Team Impul | 1:43.5670 |
| 100 | Hiroki Katou / Hidetoshi Mitsusada | Honda NSX (LA-NA2) | Team Kunimitsu With Mooncraft | 1:43.5970 |
| 37 | Takuya Kurosawa / Marco Apicella | Toyota Supra (JZA80) | Toyota Team Tom's | 1:43.7640 |
| 8 | Keiichi Tsuchiya / Toshihiro Kaneishi | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:43.9270 |
| 35 | Naoki Hattori / Shigekazu Wakisaka | Toyota Supra (JZA80) | KRAFT | 1:44.0650 |
| 16 | Daisuke Itou / Tom Coronel | Honda NSX (LA-NA2) | Dome Racing Team | 1:44.1230 |
| 36 | Takeshi Tsuchiya / Erik Comas | Toyota Supra (JZA80) | Toyota Team Tom's | 1:44.2180 |
| 25 | Seiji Ara / Jeremie Dufour | Toyota Supra (JZA80) | Team Advan Tsuchiya | 1:44.4090 |
| 18 | Ryou Michigami / Paolo Montin | Honda NSX (LA-NA2) | Dome Racing Team | 1:44.6170 |
| 88 | Kouji Yamanishi / Hisashi Wada | Lamborghini Diablo (ZA90DE068) | JLOC | 1:49.7810 |
| 71 | Tatsuya Kataoka / Keita Sawa | Toyota Celica (ZZT231) | Sigmatech Racing Team | 1:51.0310 |
| 11 | Hideshi Matsuda / Tetsuya Tanaka | Ferrari 360 Modena (GF-F360) | Team Gainer | 1:51.4260 |
| 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (GDB) | Cusco Racing | 1:51.7150 |
| 19 | Takayuki Aoki / Minoru Tanaka | Toyota Celica (ZZT231) | Racing Project Bandoh | 1:52.2560 |
| 7 | Nobuteru Taniguchi / Takashi Ooi | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:52.4390 |
| 31 | Kota Sasaki / Satoru Gotou | Toyota MR-S (GH-ZZW30) | Team Reckless | 1:52.5150 |
| 3 | Mitsuhiro Kinoshita / Masataka Yanagida | Nissan Fairlady Z (Z33) | Hasemi Motorsports | 1:52.5230 |
| 26 | Shin'ichi Yamaji / Kazuyuki Nishizawa | Porsche 996 GT3-R | Team Taisan Advan | 1:52.8000 |
| 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya | Autobacs Racing Team Aguri | 1:52.8390 |
| 55 | Eiji Yamada / Takayuki Kinoshita | Chrysler Viper GTS-R | Team Taisan Advan | 1:52.9040 |
| 34 | Seigou Nishizawa / Kouji Matsuda | Toyota MR-S (GH-ZZW30) | Dentaire Projet Racing With Apr | 1:53.4900 |
| 9 | Ichijou Suga / Katsuhiko Tsutsui | Mosler MT900R | A&S Racing | 1:53.5020 |
| 2 | Kazuho Takahashi / Akira Watanabe | Honda NSX (GH-NA2) | Verno Tokai Dream 28 | 1:53.5540 |
| 5 | Tetsuji Tamanaka / Yasutaka Hinoi | Vemac RD320R | Team B-1 | 1:53.5810 |
| 24 | Atsushi Yogou / Akihiko Asai | Porsche 996 GT3-R | Team Taisan Jr. | 1:53.9470 |
| 51 | Takeshi Shirai / Masanobu Katou | Nissan Silvia (S15) | Auto Staff Racing Team | 1:54.2550 |
| 69 | Masaru Yamagishi / Kei Itaka | Porsche 996 GT3-R | Team Gaikokuya | 1:54.7810 |
| 15 | Genji Hashimoto / Tetsuya Yamano | BMW M3 GT (E46) | Amprex Motorsport | 1:55.0020 |
| 910 | Akira Hirakawa / Yasuo Miyagawa | Porsche 996 GT3-R | 910 Racing | 1:55.6100 |
| 70 | Yoshimi Ishibashi / Isao Ihashi | Porsche 996 GT3-R | Team Gaikokuya | 1:57.5430 |