| 1 | Juichi Wakisaka / Akira Iida | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:17.8050 |
| 36 | Takeshi Tsuchiya / Erik Comas | Toyota Supra (JZA80) | Toyota Team Tom's | 1:18.2730 |
| 18 | Ryou Michigami / Sébastien Philippe | Honda NSX (LA-NA2) | Dome Racing Team | 1:18.3630 |
| 38 | Hironori Takeuchi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:18.4080 |
| 12 | Benoit Tréluyer / Yuuji Ide | Nissan Skyline GT-R (BNR34) | Team Impul | 1:18.4930 |
| 16 | Daisuke Itou / Tom Coronel | Honda NSX (LA-NA2) | Mugen | 1:18.7220 |
| 100 | Hiroki Katou / Hidetoshi Mitsusada | Honda NSX (LA-NA2) | Team Kunimitsu With Mooncraft | 1:18.7700 |
| 22 | Masami Kageyama / Richard Lyons | Nissan Skyline GT-R (BNR34) | NISMO | 1:18.8760 |
| 23 | Satoshi Motoyama / Michael Krumm | Nissan Skyline GT-R (BNR34) | NISMO | 1:18.8920 |
| 39 | Dominik Schwager / Manabu Orido | Toyota Supra (JZA80) | Toyota Team SARD | 1:18.9310 |
| 25 | Jeremie Dufour / Seiji Ara | Toyota Supra (JZA80) | Team Advan Tsuchiya | 1:18.9560 |
| 76 | Yuudai Igarashi / Eiichi Tajima | McLaren F1 GTR | Hitotsuyama Racing | 1:18.9830 |
| 64 | Tsugio Matsuda / Takashi Kogure | Honda NSX (LA-NA2) | Mobil1 Nakajima Racing | 1:19.0510 |
| 37 | Takuya Kurosawa / Marco Apicella | Toyota Supra (JZA80) | Toyota Team Tom's | 1:19.2320 |
| 35 | Naoki Hattori / Shigekazu Wakisaka | Toyota Supra (JZA80) | KRAFT | 1:19.3900 |
| 8 | Keiichi Tsuchiya / Toshihiro Kaneishi | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:19.4470 |
| 62 | Shinsuke Shibahara / Shogo Mitsuyama | Vemac RD350R | R&D Sports | 1:20.3710 |
| 88 | Naohiro Furuya / Hisashi Wada | Lamborghini Diablo (ZA90DE068) | JLOC | 1:21.4030 |
| 11 | Hideshi Matsuda / Tetsuya Tanaka | Ferrari 360 Modena (GF-F360) | Team Gainer | 1:24.6890 |
| 31 | Kota Sasaki / Satoru Gotou | Toyota MR-S (GH-ZZW30) | Team Reckless | 1:24.7770 |
| 7 | Nobuteru Taniguchi / Takashi Ooi | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:24.9590 |
| 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya | Autobacs Racing Team Aguri | 1:25.0230 |
| 2 | Kazuho Takahashi / Akira Watanabe | Honda NSX (GH-NA2) | Verno Tokai Dream 28 | 1:25.3130 |
| 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (GDB) | Cusco Racing | 1:25.6350 |
| 3 | Mitsuhiro Kinoshita / Masataka Yanagida | Nissan Fairlady Z (Z33) | Hasemi Motorsports | 1:26.0510 |
| 24 | Atsushi Yogou / Akihiko Asai | Porsche 996 GT3-R | Team Taisan Jr. | 1:26.0530 |
| 55 | Eiji Yamada / Takayuki Kinoshita | Chrysler Viper GTS-R | Team Taisan Advan | 1:26.1160 |
| 81 | Kazuki Hoshino / Tadao Uematsu | Nissan Silvia (S15) | Team Daishin | 1:26.1460 |
| 71 | Masaki Jounai / Keita Sawa | Toyota MR-S (GH-ZZW30) | Sigmatech Racing Team | 1:26.1800 |
| 26 | Shin'ichi Yamaji / Kazuyuki Nishizawa | Porsche 996 GT3-R | Team Taisan Advan | 1:26.2430 |
| 69 | Masaru Yamagishi / Kei Itaka | Porsche 996 GT3-R | Team Gaikokuya | 1:26.3440 |
| 5 | Tetsuji Tamanaka / Yasutaka Hinoi | Vemac RD320R | Team B-1 | 1:26.4380 |
| 19 | Takayuki Aoki / Minoru Tanaka | Toyota Celica (ZZT231) | Racing Project Bandoh | 1:26.9580 |
| 17 | Masahiro Matsunaga / Masaoki Nagashima | Toyota MR-S (GH-ZZW30) | Tom's Spirit | 1:27.4700 |
| 910 | Akira Hirakawa / Yasuo Miyagawa | Porsche 996 GT3-R | 910 Racing | 1:27.5500 |
| 9 | Ichijou Suga / Katsuhiko Tsutsui | Mosler MT900R | A&S Racing | 1:27.7750 |
| 15 | Genji Hashimoto / Charles Kwan | BMW M3 GT (E46) | Amprex Motorsport | 1:27.9130 |
| 21 | Yasushi Hitotsuyama / Haruhiko Matsumoto | BMW M3 GT (E46) | Hitotsuyama Racing | 1:28.2620 |
| 51 | Naofumi Omoto / Masanobu Katou | Nissan Silvia (S15) | Auto Staff Racing Team | 1:28.7910 |
| 34 | Seigou Nishizawa / Kouji Matsuda | Toyota MR-S (GH-ZZW30) | Dentaire Projet Racing With Apr | 1:29.1650 |
| 70 | Yoshimi Ishibashi / Gou Shimizu | Porsche 996 GT3-R | Team Gaikokuya | 1:29.2730 |
| 111 | Hiroya Iijima / Shigemitsu Haga | Porsche 996 GT3-R | Arktech Motorsports | 1:30.3970 |
| 10 | "Osamu" / Shin'ichi Kurashima | RGS Mirage GT-1 | Team LeyJun | 1:32.3350 |