| 16 | Daisuke Itou / Tom Coronel | Honda NSX (LA-NA2) | Dome Racing Team | 1:47.6410 |
| 1 | Juichi Wakisaka / Akira Iida | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:47.6970 |
| 38 | Hironori Takeuchi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:47.7750 |
| 12 | Benoit Tréluyer / Yuuji Ide | Nissan Skyline GT-R (BNR34) | Team Impul | 1:47.7910 |
| 22 | Masami Kageyama / Richard Lyons | Nissan Skyline GT-R (BNR34) | NISMO | 1:47.8700 |
| 64 | Tsugio Matsuda / Andre Lotterer | Honda NSX (LA-NA2) | Mobil1 Nakajima Racing | 1:47.9290 |
| 35 | Naoki Hattori / Shigekazu Wakisaka | Toyota Supra (JZA80) | KRAFT | 1:48.0010 |
| 100 | Hiroki Katou / Hidetoshi Mitsusada | Honda NSX (LA-NA2) | Team Kunimitsu With Mooncraft | 1:48.1530 |
| 8 | Keiichi Tsuchiya / Toshihiro Kaneishi | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:48.4340 |
| 39 | Dominik Schwager / Manabu Orido | Toyota Supra (JZA80) | Toyota Team SARD | 1:48.5010 |
| 18 | Ryou Michigami / Sébastien Philippe | Honda NSX (LA-NA2) | Dome Racing Team | 1:48.5250 |
| 37 | Takuya Kurosawa / Marco Apicella | Toyota Supra (JZA80) | Toyota Team Tom's | 1:48.5460 |
| 25 | Seiji Ara / Jeremie Dufour | Toyota Supra (JZA80) | Team Advan Tsuchiya | 1:48.6960 |
| 23 | Satoshi Motoyama / Michael Krumm | Nissan Skyline GT-R (BNR34) | NISMO | 1:49.8020 |
| 36 | Takeshi Tsuchiya / Erik Comas | Toyota Supra (JZA80) | Toyota Team Tom's | 1:50.0070 |
| 62 | Shinsuke Shibahara / Shogo Mitsuyama | Vemac RD350R | R&D Sports | 1:50.6060 |
| 88 | Kouji Yamanishi / Hisashi Wada | Lamborghini Diablo (ZA90DE068) | JLOC | 1:52.6760 |
| 71 | Tatsuya Kataoka / Keita Sawa | Toyota Celica (ZZT231) | Sigmatech Racing Team | 1:56.9390 |
| 3 | Mitsuhiro Kinoshita / Masataka Yanagida | Nissan Fairlady Z (Z33) | Hasemi Motorsports | 1:56.9580 |
| 51 | Naofumi Omoto / Masanobu Katou | Nissan Silvia (S15) | Auto Staff Racing Team | 1:57.5740 |
| 19 | Takayuki Aoki / Minoru Tanaka | Toyota Celica (ZZT231) | Racing Project Bandoh | 1:57.6140 |
| 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya | Autobacs Racing Team Aguri | 1:57.7540 |
| 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (GDB) | Cusco Racing | 1:57.8740 |
| 26 | Shin'ichi Yamaji / Kazuyuki Nishizawa | Porsche 996 GT3-R | Team Taisan Advan | 1:58.2430 |
| 9 | Akira Ishikawa / Katsuhiko Tsutsui | Mosler MT900R | A&S Racing | 1:58.3360 |
| 81 | Kazuki Hoshino / Tadao Uematsu | Nissan Silvia (S15) | Team Daishin | 1:58.3730 |
| 911 | Kazuyoshi Takamizawa / Tomohiko Sunako | Porsche 996 GT3-R | 910 Racing | 1:58.3750 |
| 34 | Seigou Nishizawa / Kouji Matsuda | Toyota MR-S (GH-ZZW30) | Dentaire Projet Racing With Apr | 1:58.7820 |
| 7 | Nobuteru Taniguchi / Takashi Ooi | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:58.9860 |
| 2 | Kazuho Takahashi / Akira Watanabe | Honda NSX (GH-NA2) | Verno Tokai Dream 28 | 1:59.0440 |
| 69 | Masaru Yamagishi / Kei Itaka | Porsche 996 GT3-R | Team Gaikokuya | 1:59.1600 |
| 61 | Atsushi Katsumata / Keiko Ihara | Porsche 996 GT3-R | R&D Sports | 1:59.2540 |
| 11 | Hideshi Matsuda / Tetsuya Tanaka | Ferrari 360 Modena (GF-F360) | Team Gainer | 1:59.2680 |
| 55 | Eiji Yamada / Takayuki Kinoshita | Chrysler Viper GTS-R | Team Taisan Advan | 1:59.3080 |
| 31 | Kota Sasaki / Satoru Gotou | Toyota MR-S (GH-ZZW30) | Team Reckless | 1:59.6640 |
| 5 | Tetsuji Tamanaka / Yasutaka Hinoi | Vemac RD320R | Team B-1 | 1:59.7260 |
| 24 | Atsushi Yogou / Akihiko Asai | Porsche 996 GT3-R | Team Taisan Jr. | 1:59.8460 |
| 17 | Masahiro Matsunaga / Masaoki Nagashima | Toyota MR-S (GH-ZZW30) | Tom's Spirit | 1:59.8940 |
| 15 | Genji Hashimoto / Charles Kwan | BMW M3 GT (E46) | Amprex Motorsport | 2:00.3500 |
| 910 | Akira Hirakawa / Yasuo Miyagawa | Porsche 996 GT3-R | 910 Racing | 2:00.3690 |
| 70 | Yoshimi Ishibashi / Isao Ihashi | Porsche 996 GT3-R | Team Gaikokuya | 2:01.4640 |
| 111 | Hiroya Iijima / Shigemitsu Haga | Porsche 996 GT3-R | Arktech Motorsports | 2:03.1640 |