| 61 | Hiroki Katou / Seiji Ara | Audi R8 | Audi Sport Japan Team Goh | 1:52.8560 |
| 6 | Juichi Wakisaka / Akira Iida / Shigekazu Wakisaka | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:58.0030 |
| 18 | Sébastien Philippe / Katsutomo Kaneishi / Richard Lyons | Honda NSX (GH-NA2) | Dome Mugen Project | 1:58.9330 |
| 16 | Ryou Michigami / Daisuke Itou / Hidetoshi Mitsusada | Honda NSX (GH-NA2) | Dome Mugen Project | 1:59.0310 |
| 23 | Masami Kageyama / Michael Krumm / Tetsuya Tanaka | Nissan Skyline GT-R (BNR34) | NISMO | 1:59.5710 |
| 39 | Jeremie Dufour / Manabu Orido / Nobuteru Taniguchi | Toyota Supra (JZA80) | Toyota Team SARD | 2:00.2250 |
| 88 | Hisashi Wada / Marco Apicella | Lamborghini Diablo (DE21) | JLOC | 2:05.6910 |
| 3 | Ryohei Sakaguchi / Naoki Furuya / Hidenori Kouuchi | Oscar SK5.2 Toyota | Max Racing | 2:08.2280 |
| 62 | Shinsuke Shibahara / Shogo Mitsuyama | Vemac RD320R | R&D Sport | 2:08.4880 |
| 52 | Hidetoshi Nishimura / Yoshinari Tomimoto / Masayoshi Furuya | Oscar SK5.2 Toyota | Nishimura Hidetoshi | 2:09.8140 |
| 22 | Masaki Yamamoto / Katsunori Yamamoto / Naoto Chikada | Oscar SK5.2 Toyota | Nagai Iin Motor Sport Club | 2:09.8540 |
| 5 | Tetsuji Tamanaka / Yasutaka Hinoi | Mosler MT900R | A&S Racing | 2:09.9000 |
| 71 | Masaki Jounai / Keita Sawa / Eiichi Tajima | Toyota MR-S (GH-ZZW30) | Sigmatech Racing Team | 2:10.6490 |
| 55 | Masahiro Kimoto / Romain Dumas / Xavier Pompidou | Porsche 996 GT3-RS | Kimoto Racing Team | 2:11.4840 |
| 930 | Eiji Yamada / Yasuo Miyagawa / Toshiyuki Ochiai | Porsche 930 | M's Machine Works | 2:12.1160 |
| 15 | Genji Hashimoto / Charles Kwan | BMW M3 GT (E46) | Amprex Motorsport | 2:12.4210 |
| 2 | Kazuho Takahashi / Akira Watanabe / Ichijou Suga | Honda NSX (GH-NA2) | Verno Tokai Dream 28 | 2:12.4570 |
| 911 | Akira Hirakawa / Masaya Koyama / Adam Wilcox | Porsche 996 GT3-RS | 910 Racing | 2:13.6070 |
| 9 | Masanobu Takenaka / Akihiko Tsutsumi / Tsunefumi Hioki | Porsche 996 GT3-R | Team Daikokuya | 2:13.6410 |
| 8 | Yoshimi Kaku / Kazumi Mikami / Izumi Toujou | Oscar SK5.2 Toyota | Repri Sport | 2:15.8090 |
| 70 | Yoshimi Ishibashi / Patrick van Schoote / Robert Orcutt | Porsche 996 GT3-RS | Team Gaikokuya | 2:16.8800 |
| 34 | Tomohiko Sunako / Takaya Tsubobayashi / Kei Itaka | Nissan Skyline GT-R (BNR34) | Susuki Racing Machanics | 2:18.2100 |
| 19 | Toshiaki Koshimizu / Masayuki Ueda / Takayuki Aoki | Nissan Skyline GT-R (BNR34) | JMC Racing Division | 2:18.4520 |
| 912 | Shigemitsu Haga / Hiroya Iijima / Hiroshi Wada | Porsche GT3 Cup | 910 Racing | 2:18.8690 |
| 1 | Syunji Kasuya / Katsunori Iketani / Tomiko Yoshikawa | Nissan Skyline GT-R | Oreka Technic Ideal | 2:19.4460 |
| 36 | Kazuyuki Tanaka / Seiichi Sodeyama / Keiko Inoue | Porsche 911 RSR | | 2:21.2370 |
| 20 | Nobuo Komiya / Katsuo Kobayashi / Katsuichi Itou | Mitsubishi Lancer (CT9A) | RS Ogawa | 2:21.7780 |
| 11 | Tomohiro Tomimasu / Yutaka Seki / Eiji Kouketsu | Mitsubishi Lancer (CT9A) | Shinryou Racing Team | 2:24.1030 |
| 7 | Kenjirou Katagiri / Hiroshi Hashizawa / Takahiko Hara | Lotus Elise | Wing Auto | 2:25.2330 |
| 280 | Hajime Ooshiro / Keiichi Murakami / Mitsuaki Sakai | Honda NSX | GT-ROM Net Nsx Owners Club | 2:25.8620 |
| 33 | Masami Miyoshi / Yasuo Muramatsu / Motoji Sekine | Mazda RX-7 (FD3S) | I-dea Project | 2:26.0280 |
| 14 | Eiji Satou / Souichirou Tanaka / Toshikazu Kanamori | West 936S Toyota | Team Jikanwari | 2:27.9960 |
| 45 | Takeo Asano / Tomoyuki Kasahara | Honda Integra Type R (DC5) | Asano Racing Service | 2:28.2500 |
| 73 | Masaki Takara / Manabu Yamazaki / Subaru Yamamoto | Honda Integra Type R (DC5) | Team A-One | 2:29.1690 |
| 602 | Michimasa Okada / Tatsufumi Iwatsuki / Yoshihiko Torii | Mitsubishi Lancer (CT9A) | Team Jikanwari | 2:31.8130 |