| 6 | Juichi Wakisaka / Akira Iida | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:24.3030 |
| 1 | Hironori Takeuchi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:24.4750 |
| 30 | Hideki Okada / Haruki Kurosawa | McLaren F1 GTR (19R GTR) | Team Take One | 1:24.7750 |
| 76 | Naoki Hattori / Eiichi Tajima | McLaren F1 GTR (19R GTR) | Hitotsuyama Racing | 1:24.8000 |
| 8 | Keiichi Tsuchiya / Katsutomo Kaneishi | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:24.8870 |
| 39 | Jeremie Dufour / Manabu Orido | Toyota Supra (JZA80) | Toyota Team SARD | 1:24.9800 |
| 37 | Takuya Kurosawa / Paolo Montin | Toyota Supra (JZA80) | Toyota Team Tom's | 1:25.0710 |
| 36 | Takeshi Tsuchiya / Wayne Gardner | Toyota Supra (JZA80) | Toyota Team Tom's | 1:25.1040 |
| 100 | Hidetoshi Mitsusada / Toshihiro Kaneishi | Honda NSX (LA-NA2) | Team Kunimitsu With Mooncraft | 1:25.1180 |
| 18 | Sébastien Philippe / Richard Lyons | Honda NSX (LA-NA2) | Dome Mugen Project | 1:25.2110 |
| 12 | Tetsuya Tanaka / Kazuyoshi Hoshino | Nissan Skyline GT-R (BNR34) | Team Impul | 1:25.2570 |
| 64 | Ralph Firman / Tsugio Matsuda | Honda NSX (LA-NA2) | Mobil1 Nakajima Racing | 1:25.3310 |
| 22 | Satoshi Motoyama / Michael Krumm | Nissan Skyline GT-R (BNR34) | NISMO | 1:25.3430 |
| 35 | Masahiko Kageyama / Shigekazu Wakisaka | Toyota Supra (JZA80) | KRAFT | 1:25.3930 |
| 16 | Dominik Schwager / Daisuke Itou | Honda NSX (LA-NA2) | Dome Mugen Project | 1:25.4940 |
| 23 | Erik Comas / Masami Kageyama | Nissan Skyline GT-R (BNR34) | NISMO | 1:25.5260 |
| 25 | Shin'ichi Yamaji / Geoff Lees | Toyota Supra (JZA80) | Tsuchiya Engineering | 1:25.6550 |
| 88 | Marco Apicella / Hisashi Wada | Lamborghini Diablo JGT-1 (ZA90DE068) | JLOC | 1:28.4750 |
| 2 | Kazuho Takahashi / Akira Watanabe | Honda NSX (GH-NA2) | Verno Tokai Dream 28 | 1:32.5210 |
| 19 | Minoru Tanaka / Satoru Gotou | Toyota MR-S (ZZW30) | Racing Project Bandoh | 1:32.7550 |
| 62 | Shinsuke Shibahara / Shogo Mitsuyama | Vemac RD320R | R&D Sport | 1:32.8270 |
| 15 | Genji Hashimoto / Charles Kwan | BMW M3 GT (E46) | Amprex Motorsport | 1:33.0440 |
| 71 | Masaki Jounai / Keita Sawa | Toyota MR-S (GH-ZZW30) | Sigmatech Racing Team | 1:33.0530 |
| 31 | Morio Nitta / Shinichi Takagi | Toyota MR-S (ZZW30) | ARTA With A'pex | 1:33.0950 |
| 55 | Eiji Yamada / Gou Shimizu | Chrysler Viper GTS-R | Team Taisan Advan Jr. | 1:33.1330 |
| 910 | Hideshi Matsuda / Adam Wilcox | Porsche 996 GT3-RS | 910 Racing | 1:33.1390 |
| 86 | Masaoki Nagashima / Kouji Matsuda | Toyota MR-S (ZZW30) | KRAFT | 1:33.2050 |
| 24 | Hideo Fukuyama / Mitsuhiro Kinoshita | Porsche 996 GT3-R | Team Taisan Advan | 1:33.2690 |
| 3 | Tetsuya Yamano / Masataka Yanagida | Nissan Silvia (S15) | Hasemi Motorsports | 1:33.3810 |
| 26 | Takayuki Kinoshita / Kazuyuki Nishizawa | Porsche 996 GT3-RS | Team Taisan Advan | 1:33.5800 |
| 81 | Nobuyuki Ohyagi / Takayuki Aoki | Nissan Silvia (S15) | Team Daishin | 1:33.6610 |
| 7 | Haruhiko Matsumoto / Nobuteru Taniguchi | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:33.6910 |
| 17 | Masahiro Matsunaga / Takeshi Namekawa | Toyota MR-S (ZZW30) | Tom's Spirit | 1:34.1820 |
| 360 | Seigou Nishizawa / Kota Sasaki | Ferrari 360 Modena (GF-F360) | Dentaire Projet Racing | 1:34.3480 |
| 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (E-GC8) | Cusco Racing | 1:34.4110 |
| 28 | Tomohiko Sunako / Yutaka Yamagishi | Porsche 996 GT3-RS | Team Taisan Jr. | 1:34.9240 |
| 9 | Yousuke Shimojima / Masanobu Takenaka | Porsche 996 GT3-R | Team Daikokuya | 1:35.2740 |
| 21 | Yasushi Hitotsuyama / Yasushi Kikuchi | BMW M3 GT (E46) | Hitotsuyama Racing | 1:35.4020 |
| 61 | Tsubasa Kurosawa / Yasuo Miyagawa | Porsche 996 GT3-RS | R&D Sport Ex | 1:35.4700 |
| 911 | Akira Hirakawa / Shigemitsu Haga | Porsche 996 GT3-RS | 910 Racing | 1:35.5090 |
| 5 | Tetsuji Tamanaka / Yasutaka Hinoi | Mosler MT900R | A&S Racing | 1:35.5380 |
| 63 | "Osamu" / Takamasa Nakagawa | Porsche 996 GT3-RS | R&D Sport | 1:35.6880 |
| 70 | Yoshimi Ishibashi / Patrick van Schoote | Porsche 996 GT3-RS | Team Gaikokuya | 1:37.0300 |
| 4 | Toshiyuki Yamamoto / Izumi Yoshida | Chevrolet Corvette (C-4) | Zipspeed | 1:48.2150 |