| 6 | Juichi Wakisaka / Akira Iida | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:19.2590 |
| 38 | Yuuji Tachikawa / Seiji Ara | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:19.3230 |
| 25 | Manabu Orido / Dominik Schwager | Toyota Supra (JZA80) | Team Advan Tsuchiya | 1:19.4460 |
| 22 | Masami Kageyama / Michael Krumm | Nissan Fairlady Z (Z33) | NISMO | 1:19.5980 |
| 12 | Benoit Tréluyer / Yuuji Ide | Nissan Fairlady Z (Z33) | Team Impul | 1:19.6180 |
| 39 | Jeremie Dufour / André Couto | Toyota Supra (JZA80) | Toyota Team SARD | 1:19.8920 |
| 36 | Takeshi Tsuchiya / Marco Apicella | Toyota Supra (JZA80) | Toyota Team Tom's | 1:19.9060 |
| 37 | James Courtney / Tatsuya Kataoka | Toyota Supra (JZA80) | Toyota Team Tom's | 1:19.9360 |
| 32 | Tsugio Matsuda / Andre Lotterer | Honda NSX (LA-NA2) | Epson Nakajima Racing | 1:19.9670 |
| 1 | Satoshi Motoyama / Richard Lyons | Nissan Fairlady Z (Z33) | NISMO | 1:20.2890 |
| 3 | Toshihiro Kaneishi / Erik Comas | Nissan Fairlady Z (Z33) | Hasemi Motorsport | 1:20.3060 |
| 35 | Naoki Hattori / Shigekazu Wakisaka | Toyota Supra (JZA80) | KRAFT | 1:20.3580 |
| 8 | Katsutomo Kaneishi / Daisuke Itou | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:20.4230 |
| 18 | Ryou Michigami / Sébastien Philippe | Honda NSX (LA-NA2) | Dome Racing Team | 1:20.4840 |
| 100 | Shinji Nakano / Hiroki Katou | Honda NSX (LA-NA2) | Team Kunimitsu With Moon Craft | 1:20.8350 |
| 16 | Tetsuya Yamano / Hiroyuki Yagi | Honda NSX (LA-NA2) | M-Tec Co.Ltd. | 1:24.3360 |
| 21 | Hidetoshi Mitsusada / Tadao Uematsu | Ferrari 550 Maranello GTS | Hitotsuyama Racing | 1:24.7630 |
| 11 | Hideshi Matsuda / Ichijou Suga | Ferrari 360 Modena (GF-F360) | Team Gainer | 1:24.8720 |
| 19 | Takayuki Aoki / Nobuteru Taniguchi | Toyota Celica (ZZT231) | Racing Project Bandoh | 1:25.0810 |
| 31 | Minoru Tanaka / Kouji Matsuda | Toyota MR-S (GH-ZZW30) | A'pex With Apr | 1:25.1210 |
| 63 | "Osamu" / Hiroki Yoshimoto | Vemac RD320R | Team LeyJun | 1:25.1430 |
| 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya (SA9VGR) | Autobacs Racing Team Aguri | 1:25.2320 |
| 10 | Tetsuya Tanaka / Atsushi Yogou | Ferrari 360 Modena (GF-F360) | Team Gainer | 1:25.3000 |
| 7 | Shin'ichi Yamaji / Hiroyuki Iiri | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:25.3110 |
| 52 | Hironori Takeuchi / Seigou Nishizawa | Toyota Celica (ZZT231) | Toyota Team Cerumo | 1:25.3730 |
| 30 | Kota Sasaki / Satoru Gotou | Toyota MR-S (GH-ZZW30) | Team Reckless | 1:25.5880 |
| 81 | Masataka Yanagida / Naofumi Omoto | Nissan Fairlady Z (Z33) | Team Daishin | 1:25.6380 |
| 80 | Mitsuhiro Kinoshita / Kazuki Hoshino | Nissan Fairlady Z (Z33) | Team Daishin | 1:25.8990 |
| 5 | Tetsuji Tamanaka / Yasutaka Hinoi | Vemac RD320R | Team Mach | 1:26.2970 |
| 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (GDB) | Cusco Racing | 1:26.3210 |
| 17 | Masahiro Matsunaga / Masaoki Nagashima | Toyota Celica (ZZT231) | Spirit Motorsport | 1:26.4690 |
| 20 | Takashi Inoue / Yasuo Miyagawa | Porsche 996 GT3-RSR | Hitotsuyama Racing | 1:26.6410 |
| 111 | Hiroya Iijima / Takashi Ooi | Porsche 968 (E-968) | Arktech Motorsports | 1:27.0210 |
| 2 | Kazuho Takahashi / Akira Watanabe | Honda NSX (GH-NA2) | Verno Tokai Dream 28 | 1:27.1700 |
| 9 | Gou Shimizu / Shin'ya Hosokawa | Mosler MT900R | A&S Racing | 1:27.3740 |
| 72 | Akira Hirakawa / Masaki Jounai | Porsche 996 GT3-RS | Team Gaikokuya | 1:27.5070 |
| 112 | Keita Sawa / Akihiko Tsutsumi | Porsche 996 GT3-RS | Arktech Motorsports | 1:27.6040 |
| 26 | Kaoru Ijiri / Yutaka Yamagishi | Porsche 996 GT3-RS | Team Taisan | 1:27.6630 |
| 910 | Kazuyoshi Takamizawa / Tomohiko Sunako | Porsche 996 GT3-RS | 910 Racing | 1:27.8050 |
| 51 | Masanobu Katou / Katsuhiko Tsutsui | Nissan Silvia (S15) | Auto Staff Racing | 1:27.8550 |
| 70 | Yoshimi Ishibashi / Hiromi Kozono | Porsche 996 GT3-RS | Team Gaikokuya | 1:29.4330 |