| 1 | Hironori Takeuchi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:24.7290 |
| 25 | Seiji Ara / Shin'ichi Yamaji | Toyota Supra (JZA80) | Tsuchiya Engineering | 1:24.9200 |
| 22 | Satoshi Motoyama / Michael Krumm | Nissan Skyline GT-R (BNR34) | NISMO | 1:25.1790 |
| 36 | Takeshi Tsuchiya / Wayne Gardner | Toyota Supra (JZA80) | Toyota Team Tom's | 1:25.2050 |
| 18 | Sébastien Philippe / Richard Lyons | Honda NSX (LA-NA2) | Dome Mugen Project | 1:25.3590 |
| 37 | Takuya Kurosawa / Paolo Montin | Toyota Supra (JZA80) | Toyota Team Tom's | 1:25.4430 |
| 76 | Naoki Hattori / Eiichi Tajima | McLaren F1 GTR (19R GTR) | Hitotsuyama Racing | 1:25.4980 |
| 100 | Hiroki Katou / Hidetoshi Mitsusada | Honda NSX (LA-NA2) | Team Kunimitsu With Mooncraft | 1:25.5080 |
| 33 | Masahiko Kondou / Hayanari Shimoda | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:25.6160 |
| 16 | Ryou Michigami / Daisuke Itou | Honda NSX (LA-NA2) | Dome Mugen Project | 1:25.6850 |
| 6 | Juichi Wakisaka / Akira Iida | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:25.7350 |
| 39 | Jeremie Dufour / Manabu Orido | Toyota Supra (JZA80) | Toyota Team SARD | 1:25.7810 |
| 30 | Hideki Okada / Haruki Kurosawa | McLaren F1 GTR (19R GTR) | Team Take One | 1:25.8070 |
| 8 | Keiichi Tsuchiya / Katsutomo Kaneishi | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:25.9020 |
| 64 | Tsugio Matsuda / Ralph Firman | Honda NSX (LA-NA2) | Mobil1 Nakajima Racing | 1:26.0730 |
| 35 | Masahiko Kageyama / Shigekazu Wakisaka | Toyota Supra (JZA80) | KRAFT | 1:26.0920 |
| 23 | Masami Kageyama / Erik Comas | Nissan Skyline GT-R (BNR34) | NISMO | 1:26.4750 |
| 12 | Kazuyoshi Hoshino / Tetsuya Tanaka | Nissan Skyline GT-R (BNR34) | Team Impul | 1:27.7160 |
| 88 | Marco Apicella / Hisashi Wada | Lamborghini Diablo JGT-1 (ZA90DE068) | JLOC | 1:27.8300 |
| 62 | Shinsuke Shibahara / Shogo Mitsuyama | Vemac RD320R | R&D Sport | 1:32.5970 |
| 24 | Hideo Fukuyama / Mitsuhiro Kinoshita | Porsche 996 GT3-R | Team Taisan Advan | 1:33.0400 |
| 71 | Masaki Jounai / Keita Sawa | Toyota MR-S (GH-ZZW30) | Sigmatech Racing Team | 1:33.0720 |
| 81 | Nobuyuki Ohyagi / Takayuki Aoki | Nissan Silvia (S15) | Team Daishin | 1:33.1140 |
| 26 | Atsushi Yogou / Kazuyuki Nishizawa | Porsche 996 GT3-RS | Team Taisan Advan | 1:33.2050 |
| 3 | Tetsuya Yamano / Masataka Yanagida | Nissan Silvia (S15) | Hasemi Motorsports | 1:33.2620 |
| 910 | Hideshi Matsuda / Adam Wilcox | Porsche 996 GT3-RS | 910 Racing | 1:33.3510 |
| 31 | Morio Nitta / Shinichi Takagi | Toyota MR-S (ZZW30) | ARTA With A'pex | 1:33.3660 |
| 2 | Kazuho Takahashi / Akira Watanabe | Honda NSX (GH-NA2) | Verno Tokai Dream 28 | 1:33.6660 |
| 15 | Genji Hashimoto / Charles Kwan | BMW M3 GT (E46) | Amprex Motorsport | 1:33.9420 |
| 55 | Eiji Yamada / Gou Shimizu | Chrysler Viper GTS-R | Team Taisan Advan Jr. | 1:33.9490 |
| 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (E-GC8) | Cusco Racing | 1:33.9700 |
| 86 | Masaoki Nagashima / Kouji Matsuda | Toyota MR-S (ZZW30) | KRAFT | 1:34.3430 |
| 19 | Minoru Tanaka / Satoru Gotou | Toyota MR-S (ZZW30) | Racing Project Bandoh | 1:34.3640 |
| 5 | Tetsuji Tamanaka / Yasutaka Hinoi | Mosler MT900R | A&S Racing | 1:34.5060 |
| 7 | Haruhiko Matsumoto / Nobuteru Taniguchi | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:34.5430 |
| 17 | Masahiro Matsunaga / Takeshi Namekawa | Toyota MR-S (ZZW30) | Tom's Spirit | 1:34.7210 |
| 61 | Yasuo Miyagawa / Atsushi Katsumata | Porsche 996 GT3-RS | R&D Sport Ex | 1:34.7840 |
| 28 | Yukihiro Hane / Yutaka Yamagishi | Porsche 996 GT3-RS | Team Taisan Jr. | 1:35.0310 |
| 63 | "Osamu" / Takamasa Nakagawa | Porsche 996 GT3-RS | R&D Sport | 1:35.0700 |
| 21 | Yasushi Hitotsuyama / Yasushi Kikuchi | BMW M3 GT (E46) | Hitotsuyama Racing | 1:35.8760 |
| 51 | Naofumi Omoto / Masanobu Katou | Nissan Silvia (S15) | Auto Staff Racing Team | 1:35.9020 |
| 9 | Masanobu Takenaka / Akihiko Tsutsumi | Porsche 996 GT3-R | Team Daikokuya | 1:36.1650 |
| 911 | Akira Hirakawa / Tomohiko Sunako | Porsche 996 GT3-RS | 910 Racing | 1:36.4670 |
| 66 | Tetsuya Shimizu / Shinji Abe | Mazda RX-7 (FD3S) | Team Revolution | 1:36.6130 |
| 70 | Yoshimi Ishibashi / Patrick van Schoote | Porsche 996 GT3-RS | Team Gaikokuya | 1:36.9680 |