| 38 | Hironori Takeuchi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:24.5520 |
| 25 | Jeremie Dufour / Seiji Ara | Toyota Supra (JZA80) | Team Advan Tsuchiya | 1:24.9710 |
| 12 | Yuuji Ide / Benoit Tréluyer | Nissan Skyline GT-R (BNR34) | Team Impul | 1:25.0340 |
| 37 | Takuya Kurosawa / Marco Apicella | Toyota Supra (JZA80) | Toyota Team Tom's | 1:25.0830 |
| 22 | Masami Kageyama / Richard Lyons | Nissan Skyline GT-R (BNR34) | NISMO | 1:25.1300 |
| 39 | Dominik Schwager / Manabu Orido | Toyota Supra (JZA80) | Toyota Team SARD | 1:25.1580 |
| 36 | Erik Comas / Takeshi Tsuchiya | Toyota Supra (JZA80) | Toyota Team Tom's | 1:25.1910 |
| 18 | Sébastien Philippe / Ryou Michigami | Honda NSX (LA-NA2) | Dome Racing Team | 1:25.1970 |
| 35 | Naoki Hattori / Shigekazu Wakisaka | Toyota Supra (JZA80) | KRAFT | 1:25.2820 |
| 23 | Satoshi Motoyama / Michael Krumm | Nissan Skyline GT-R (BNR34) | NISMO | 1:25.4050 |
| 1 | Akira Iida / Juichi Wakisaka | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:25.4540 |
| 100 | Hiroki Katou / Hidetoshi Mitsusada | Honda NSX (LA-NA2) | Team Kunimitsu With Mooncraft | 1:25.9350 |
| 64 | Andre Lotterer / Tsugio Matsuda | Honda NSX (LA-NA2) | Mobil1 Nakajima Racing | 1:26.1410 |
| 8 | Katsutomo Kaneishi / Keiichi Tsuchiya | Honda NSX (LA-NA2) | Autobacs Racing Team Aguri | 1:26.4390 |
| 76 | Eiichi Tajima / Haruki Kurosawa | McLaren F1 GTR (4S70) | Hitotsuyama Racing | 1:26.6840 |
| 62 | Shinsuke Shibahara / Shogo Mitsuyama | Vemac RD350R | R&D Sports | 1:27.7720 |
| 88 | Hisashi Wada / Kouji Yamanishi | Lamborghini Diablo (ZA90DE068) | JLOC | 1:29.3150 |
| 19 | Minoru Tanaka / Takayuki Aoki | Toyota Celica (ZZT231) | Racing Project Bandoh | 1:32.5040 |
| 55 | Takayuki Kinoshita / Eiji Yamada | Chrysler Viper GTS-R | Team Taisan Advan | 1:32.7120 |
| 3 | Masataka Yanagida / Mitsuhiro Kinoshita | Nissan Fairlady Z (Z33) | Hasemi Motorsports | 1:32.9130 |
| 11 | Hideshi Matsuda / Tetsuya Tanaka | Ferrari 360 Modena (GF-F360) | Team Gainer | 1:33.0970 |
| 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya | Autobacs Racing Team Aguri | 1:33.2530 |
| 31 | Satoru Gotou / Kota Sasaki | Toyota MR-S (GH-ZZW30) | Team Reckless | 1:33.4210 |
| 71 | Keita Sawa / Masaki Jounai | Toyota MR-S (GH-ZZW30) | Sigmatech Racing Team | 1:33.4540 |
| 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (GDB) | Cusco Racing | 1:33.5180 |
| 69 | Kei Itaka / Masaru Yamagishi | Porsche 996 GT3-R | Team Gaikokuya | 1:33.5320 |
| 24 | Akihiko Asai / Atsushi Yogou | Porsche 996 GT3-R | Team Taisan Jr. | 1:33.6400 |
| 81 | Tadao Uematsu / Kazuki Hoshino | Nissan Silvia (S15) | Team Daishin | 1:33.6540 |
| 2 | Kazuho Takahashi / Akira Watanabe | Honda NSX (GH-NA2) | Verno Tokai Dream 28 | 1:33.6780 |
| 51 | Masanobu Katou / Naofumi Omoto | Nissan Silvia (S15) | Auto Staff Racing Team | 1:33.6860 |
| 9 | Katsuhiko Tsutsui / Ichijou Suga | Mosler MT900R | A&S Racing | 1:33.7110 |
| 5 | Tetsuji Tamanaka / Yasutaka Hinoi | Vemac RD320R | Team B-1 | 1:33.7350 |
| 34 | Seigou Nishizawa / Kouji Matsuda | Toyota MR-S (GH-ZZW30) | Dentaire Projet Racing With Apr | 1:33.7470 |
| 17 | Masaoki Nagashima / Masahiro Matsunaga | Toyota MR-S (GH-ZZW30) | Tom's Spirit | 1:33.9140 |
| 7 | Takashi Ooi / Nobuteru Taniguchi | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:34.1070 |
| 910 | Yasuo Miyagawa / Akira Hirakawa | Porsche 996 GT3-R | 910 Racing | 1:34.4550 |
| 26 | Kazuyuki Nishizawa / Shin'ichi Yamaji | Porsche 996 GT3-R | Team Taisan Advan | 1:34.4840 |
| 911 | Tomohiko Sunako / Kazuyoshi Takamizawa | Porsche 996 GT3-R | 910 Racing | 1:34.4970 |
| 15 | Genji Hashimoto / Charles Kwan | BMW M3 GT (E46) | Amprex Motorsport | 1:35.4730 |
| 70 | Gou Shimizu / Yoshimi Ishibashi | Porsche 996 GT3-R | Team Gaikokuya | 1:35.5100 |
| 10 | Tatsuya Mizutani / "Osamu" | RGS Mirage GT-1 | Team LeyJun | 1:35.6130 |
| 111 | Hiroya Iijima / Shigemitsu Haga | Porsche 996 GT3-R | Arktech Motorsports | 1:38.4670 |
| 21 | Yasushi Hitotsuyama / Haruhiko Matsumoto | BMW M3 GT (E46) | Hitotsuyama Racing | 1:39.8690 |