| 1st | 18 | Juichi Wakisaka / Katsutomo Kaneishi | Honda NSX (GH-NA2) | Dome Mugen Project | 1:25.0170 |
| 2nd | 6 | Hideki Noda / Wayne Gardner | Toyota Supra (JZA80) | Esso Ultron Toyota Team Le Mans | 1:25.1360 |
| 3rd | 2 | Ukyou Katayama / Michael Krumm | Nissan Skyline GT-R (BNR34) | NISMO | 1:25.5080 |
| 4th | 21 | Yasushi Hitotsuyama / Akihiko Nakaya | McLaren F1 GTR | Hitotsuyama Racing | 1:25.5710 |
| 5th | 38 | Hironori Takeuchi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:25.7720 |
| 6th | 16 | Osamu Nakako / Ryou Michigami | Honda NSX (GH-NA2) | Dome Mugen Project | 1:26.0570 |
| 7th | 100 | Akira Iida / Naoki Hattori | Honda NSX (GH-NA2) | Team Kunimitsu With Mooncraft | 1:26.2810 |
| 8th | 30 | Youji Yamada / Hideki Okada | McLaren F1 GTR | Team Take One | 1:26.2820 |
| 9th | 12 | Kazuyoshi Hoshino / Satoshi Motoyama | Nissan Skyline GT-R (BNR34) | Team Impul | 1:26.3800 |
| 10th | 37 | Seiji Ara / Toshio Suzuki | Toyota Supra (JZA80) | Toyota Castrol Team Tom's | 1:26.4860 |
| 11th | 32 | Takayuki Kinoshita / Masahiko Kondou | Toyota Supra (JZA80) | cdma One Toyota Team Cerumo With Key's | 1:26.4900 |
| 12th | 64 | Daisuke Itou / Dominik Schwager | Honda NSX (E-NA2) | Mobil1 Nakajima Racing | 1:26.5600 |
| 13th | 1 | Erik Comas / Masami Kageyama | Nissan Skyline GT-R (BNR34) | NISMO | 1:26.6320 |
| 14th | 8 | Aguri Suzuki / Keiichi Tsuchiya | Honda NSX (E-NA2) | Autobacs Racing Team Aguri | 1:26.6640 |
| 15th | 36 | Masanori Sekiya / Takeshi Tsuchiya | Toyota Supra (JZA80) | Toyota Castrol Team Tom's | 1:26.6860 |
| 16th | 3 | Masahiro Hasemi / Tetsuya Tanaka | Nissan Skyline GT-R (BNR34) | Hasemi Motorsports | 1:26.8430 |
| 17th | 35 | Shin'ichi Yamaji / Pierre-Henri Raphanel | Toyota Supra (JZA80) | Matsumotokiyoshi Team Tom's | 1:26.9820 |
| 18th | 25 | Mitsuhiro Kinoshita / Manabu Orido | Toyota Supra (JZA80) | Endless+Tsuchiya Engineering | 1:27.1100 |
| 19th | 39 | Masahiko Kageyama / Ralph Firman | Toyota Supra (JZA80) | Toyota Team SARD | 1:27.2910 |
| 20th | 88 | Naohiro Furuya / Tsuyoshi Takahashi | Lamborghini Diablo (ZA90DE068) | JLOC | 1:28.1970 |
| 21st | 69 | Dilantha Malagamuwa / Steve Young | Mirage GT1 Chevrolet | Team Sri Lanka | 1:37.2580 |
| 22nd | 55 | Hiroaki Suga / Shinsuke Shibahara | Chrysler Viper GTS-R | Team Taisan | no time |
| 23rd | 26 | Hideshi Matsuda / Hideo Fukuyama | Porsche 996 GT3-R | Team Taisan Jr. With Advan | 1:33.5890 |
| 24th | 910 | Atsushi Yogou / Hisashi Wada | Porsche 996 GT3-R | 910 Racing | 1:33.6540 |
| 25th | 86 | Minoru Tanaka / Kouji Matsuda | Toyota Trueno (AE86) | Kraft | 1:33.9320 |
| 26th | 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (GC4) | Cusco Racing | 1:33.9730 |
| 27th | 19 | Shigekazu Wakisaka / Takahiko Hara | Toyota Celica (ST205) | Racing Project Bandoh | 1:34.1390 |
| 28th | 911 | Masamitsu Ishihara / Tomohiko Sunako | Porsche 996 GT3-R | 910 Racing | 1:34.3610 |
| 29th | 31 | Morio Nitta / Yuudai Igarashi | Toyota MR-S (GH-ZZW30) | Super Autobacs A'pex MR-S | 1:34.3770 |
| 30th | 7 | Haruhiko Matsumoto / Tetsuya Yamano | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:34.4960 |
| 31st | 81 | Nobuyuki Ohyagi / Takayuki Aoki | Nissan Silvia (S15) | Team Daishin | 1:34.5210 |
| 32nd | 10 | Yasutaka Hinoi / Yutaka Yamagishi | Porsche 911 GT2 | Ability Motorsports | 1:35.8290 |
| 33rd | 51 | Seiichi Sodeyama / Eiji Yamada | Nissan Silvia (S14) | Auto Staff Racing Team | 1:35.8530 |
| 34th | 111 | Jun'ichi Ikura / Yuusei Maki | Ferrari F355 | Team Gainer | 1:35.3190 |
| 35th | 9 | Yukihiro Hane / Tsunefumi Hioki | Porsche 993 RSR 3.8 | Team Daikokuya | 1:36.4460 |
| 36th | 71 | Masaki Jounai / Naohiro Kawano | Porsche 911 GT2 | Sigmatech Racing Team | 1:37.2130 |
| 37th | 24 | Kazuyuki Nishizawa / Marco Apicella | Porsche 986 Boxster | MTCI Racing Team | 1:37.3960 |
| 38th | 70 | Yoshimi Ishibashi / Patrick van Schoote | Porsche 911 GT2 | Team Gaikokuya | 1:38.4390 |
| 39th | 11 | Kengo Kitaura / Hikaru Miyagi | Porsche 911 GT2 | Ability Motorsports | 1:40.6640 |