| 38 | Hironori Takeuchi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:24.1880 |
| 37 | Takuya Kurosawa / Marco Apicella | Toyota Supra (JZA80) | Toyota Team Tom's | 1:24.2990 |
| 36 | Takeshi Tsuchiya / Erik Comas | Toyota Supra (JZA80) | Toyota Team Tom's | 1:24.4150 |
| 1 | Juichi Wakisaka / Akira Iida | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:24.5350 |
| 35 | Naoki Hattori / Shigekazu Wakisaka | Toyota Supra (JZA80) | KRAFT | 1:24.5600 |
| 25 | Jeremie Dufour / Seiji Ara | Toyota Supra (JZA80) | Team Advan Tsuchiya | 1:24.6950 |
| 23 | Satoshi Motoyama / Michael Krumm | Nissan Skyline GT-R (BNR34) | NISMO | 1:24.7060 |
| 22 | Masami Kageyama / Richard Lyons | Nissan Skyline GT-R (BNR34) | NISMO | 1:25.0460 |
| 18 | Ryou Michigami / Sébastien Philippe | Honda NSX (LA-NA2) | Dome Racing Team | 1:25.0470 |
| 39 | Dominik Schwager / Manabu Orido | Toyota Supra (JZA80) | Toyota Team SARD | 1:25.3850 |
| 16 | Daisuke Itou / Tom Coronel | Honda NSX (LA-NA2) | Dome Racing Team | 1:25.3930 |
| 64 | Tsugio Matsuda / Andre Lotterer | Honda NSX (LA-NA2) | Mobil1 Nakajima Racing | 1:25.5340 |
| 100 | Hiroki Katou / Hidetoshi Mitsusada | Honda NSX (LA-NA2) | Team Kunimitsu With Mooncraft | 1:25.6280 |
| 12 | Benoit Tréluyer / Yuuji Ide | Nissan Skyline GT-R (BNR34) | Team Impul | 1:25.6540 |
| 62 | Shinsuke Shibahara / Shogo Mitsuyama | Vemac RD350R | R&D Sports | 1:25.8610 |
| 76 | Haruki Kurosawa / Eiichi Tajima | McLaren F1 GTR (4S70) | Hitotsuyama Racing | 1:26.1100 |
| 8 | Keiichi Tsuchiya / Toshihiro Kaneishi | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:26.1570 |
| 88 | Kouji Yamanishi / Hisashi Wada | Lamborghini Diablo (ZA90DE068) | JLOC | 1:28.2760 |
| 19 | Takayuki Aoki / Minoru Tanaka | Toyota Celica (ZZT231) | Racing Project Bandoh | 1:31.5240 |
| 71 | Masaki Jounai / Keita Sawa | Toyota MR-S (GH-ZZW30) | Sigmatech Racing Team | 1:31.7480 |
| 81 | Kazuki Hoshino / Tadao Uematsu | Nissan Silvia (S15) | Team Daishin | 1:32.1600 |
| 9 | Ichijou Suga / Katsuhiko Tsutsui | Mosler MT900R | A&S Racing | 1:32.2840 |
| 31 | Kota Sasaki / Satoru Gotou | Toyota MR-S (GH-ZZW30) | Team Reckless | 1:32.3260 |
| 55 | Eiji Yamada / Takayuki Kinoshita | Chrysler Viper GTS-R | Team Taisan Advan | 1:32.3620 |
| 24 | Atsushi Yogou / Akihiko Asai | Porsche 996 GT3R | Team Taisan Jr. | 1:32.4190 |
| 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya | Autobacs Racing Team Aguri | 1:32.5120 |
| 26 | Shin'ichi Yamaji / Kazuyuki Nishizawa | Porsche 996 GT3-R | Team Taisan Advan | 1:32.5610 |
| 34 | Seigou Nishizawa / Kouji Matsuda | Toyota MR-S (GH-ZZW30) | Dentaire Projet Racing With Apr | 1:32.6650 |
| 3 | Mitsuhiro Kinoshita / Masataka Yanagida | Nissan Fairlady Z (Z33) | Hasemi Motorsports | 1:32.7040 |
| 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (GDB) | Cusco Racing | 1:32.8210 |
| 11 | Hideshi Matsuda / Tetsuya Tanaka | Ferrari 360 Modena (GF-F360) | Team Gainer | 1:33.0740 |
| 69 | Masaru Yamagishi / Kei Itaka | Porsche 996 GT3-R | Team Gaikokuya | 1:33.3160 |
| 5 | Tetsuji Tamanaka / Yasutaka Hinoi | Vemac RD320R | Team B-1 | 1:33.4530 |
| 17 | Masahiro Matsunaga / Masaoki Nagashima | Toyota MR-S (GH-ZZW30) | Tom's Spirit | 1:33.4630 |
| 51 | Naofumi Omoto / Masanobu Katou | Nissan Silvia (S15) | Auto Staff Racing Team | 1:33.6720 |
| 2 | Kazuho Takahashi / Akira Watanabe | Honda NSX (GH-NA2) | Verno Tokai Dream 28 | 1:33.7580 |
| 7 | Nobuteru Taniguchi / Takashi Ooi | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:33.9340 |
| 910 | Akira Hirakawa / Yasuo Miyagawa | Porsche 996 GT3-R | 910 Racing | 1:34.0510 |
| 15 | Genji Hashimoto / Charles Kwan | BMW M3 GT (E46) | Amprex Motorsport | 1:34.1330 |
| 61 | Atsushi Katsumata / Keiko Ihara | Porsche 996 GT3-R | R&D Sports | 1:34.7060 |
| 14 | Tengku Djan Ley / Tetsuya Yamano | Mazda RX-7 (FD3S) | Amprex Motorsport | 1:35.4800 |
| 21 | Yasushi Hitotsuyama / Haruhiko Matsumoto | BMW M3 GT (E46) | Hitotsuyama Racing | 1:35.6570 |
| 70 | Yoshimi Ishibashi / Hiroshi Wada | Porsche 996 GT3-R | Team Gaikokuya | 1:37.0560 |
| 111 | Hiroya Iijima / Shigemitsu Haga | Porsche 996 GT3-R | Arktech Motorsports | 1:37.4560 |
| 10 | "Osamu" / Naohiro Furuya | Porsche 996 GT3-R | Team LeyJun | 1:38.6960 |