| 61 | Hiroki Katou / Seiji Ara | Audi R8 | Audi Sport Japan Team Goh | 1:57.6030 |
| 6 | Juichi Wakisaka / Akira Iida / Shigekazu Wakisaka | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:58.0450 |
| 18 | Sébastien Philippe / Katsutomo Kaneishi / Richard Lyons | Honda NSX (GH-NA2) | Dome Mugen Project | 1:58.4360 |
| 16 | Ryou Michigami / Daisuke Itou / Hidetoshi Mitsusada | Honda NSX (GH-NA2) | Dome Mugen Project | 1:59.0080 |
| 23 | Masami Kageyama / Michael Krumm / Tetsuya Tanaka | Nissan Skyline GT-R (BNR34) | NISMO | 2:00.5480 |
| 39 | Jeremie Dufour / Manabu Orido / Nobuteru Taniguchi | Toyota Supra (JZA80) | Toyota Team SARD | 2:02.6140 |
| 88 | Hisashi Wada / Marco Apicella | Lamborghini Diablo (DE21) | JLOC | 2:06.5270 |
| 62 | Shinsuke Shibahara / Shogo Mitsuyama | Vemac RD320R | R&D Sport | 2:08.1900 |
| 3 | Ryohei Sakaguchi / Naoki Furuya / Hidenori Kouuchi | Oscar SK5.2 Toyota | Max Racing | 2:08.2300 |
| 5 | Tetsuji Tamanaka / Yasutaka Hinoi | Mosler MT900R | A&S Racing | 2:10.7980 |
| 9 | Masanobu Takenaka / Akihiko Tsutsumi / Tsunefumi Hioki | Porsche 996 GT3-R | Team Daikokuya | 2:12.4650 |
| 71 | Masaki Jounai / Keita Sawa / Eiichi Tajima | Toyota MR-S (GH-ZZW30) | Sigmatech Racing Team | 2:12.7590 |
| 2 | Kazuho Takahashi / Akira Watanabe / Ichijou Suga | Honda NSX (GH-NA2) | Verno Tokai Dream 28 | 2:12.9810 |
| 22 | Masaki Yamamoto / Katsunori Yamamoto / Naoto Chikada | Oscar SK5.2 Toyota | Nagai Iin Motor Sport Club | 2:13.1660 |
| 15 | Genji Hashimoto / Charles Kwan | BMW M3 GT (E46) | Amprex Motorsport | 2:13.5620 |
| 55 | Masahiro Kimoto / Romain Dumas / Xavier Pompidou | Porsche 996 GT3-RS | Kimoto Racing Team | 2:13.6190 |
| 52 | Hidetoshi Nishimura / Yoshinari Tomimoto / Masayoshi Furuya | Oscar SK5.2 Toyota | Nishimura Hidetoshi | 2:14.3450 |
| 8 | Yoshimi Kaku / Kazumi Mikami / Izumi Toujou | Oscar SK5.2 Toyota | Repri Sport | 2:15.0760 |
| 911 | Akira Hirakawa / Masaya Koyama / Adam Wilcox | Porsche 996 GT3-RS | 910 Racing | 2:15.0880 |
| 930 | Eiji Yamada / Yasuo Miyagawa / Toshiyuki Ochiai | Porsche 930 | M's Machine Works | 2:17.3940 |
| 19 | Toshiaki Koshimizu / Masayuki Ueda / Takayuki Aoki | Nissan Skyline GT-R (BNR34) | JMC Racing Division | 2:17.7060 |
| 34 | Tomohiko Sunako / Takaya Tsubobayashi / Kei Itaka | Nissan Skyline GT-R (BNR34) | Susuki Racing Machanics | 2:18.9150 |
| 1 | Syunji Kasuya / Katsunori Iketani / Tomiko Yoshikawa | Nissan Skyline GT-R | Oreka Technic Ideal | 2:19.7360 |
| 20 | Nobuo Komiya / Katsuo Kobayashi / Katsuichi Itou | Mitsubishi Lancer (CT9A) | RS Ogawa | 2:23.0330 |
| 14 | Eiji Satou / Souichirou Tanaka / Toshikazu Kanamori | West 936S Toyota | Team Jikanwari | 2:24.8130 |
| 33 | Masami Miyoshi / Yasuo Muramatsu / Motoji Sekine | Mazda RX-7 (FD3S) | I-dea Project | 2:25.0080 |
| 11 | Tomohiro Tomimasu / Yutaka Seki / Eiji Kouketsu | Mitsubishi Lancer (CT9A) | Shinryou Racing Team | 2:25.6630 |
| 912 | Shigemitsu Haga / Hiroya Iijima / Hiroshi Wada | Porsche GT3 Cup | 910 Racing | 2:27.6990 |
| 73 | Masaki Takara / Manabu Yamazaki / Subaru Yamamoto | Honda Integra Type R (DC5) | Team A-One | 2:30.4400 |
| 280 | Hajime Ooshiro / Keiichi Murakami / Mitsuaki Sakai | Honda NSX | GT-ROM Net Nsx Owners Club | 2:31.1450 |
| 7 | Kenjirou Katagiri / Hiroshi Hashizawa / Takahiko Hara | Lotus Elise | Wing Auto | 2:32.2040 |
| 602 | Michimasa Okada / Tatsufumi Iwatsuki / Yoshihiko Torii | Mitsubishi Lancer (CT9A) | Team Jikanwari | 2:36.6220 |