| 8 | Ralph Firman / Daisuke Itou | Honda NSX (LA-NA2) | Team Honda Racing | 1:53.3280 |
| 22 | Masataka Yanagida / Michael Krumm | Nissan Fairlady Z (Z33) | NISMO | 1:53.4070 |
| 25 | Manabu Orido / Dominik Schwager | Toyota Supra (JZA80) | Team Advan Tsuchiya | 1:53.4820 |
| 18 | Takashi Kogure / Ryou Michigami | Honda NSX (LA-NA2) | Team Honda Racing | 1:53.6710 |
| 3 | Erik Comas / Toshihiro Kaneishi | Nissan Fairlady Z (Z33) | Hasemi Motorsport | 1:53.8550 |
| 12 | Yuuji Ide / Benoit Tréluyer | Nissan Fairlady Z (Z33) | Team Impul | 1:53.8930 |
| 1 | Satoshi Motoyama / Richard Lyons | Nissan Fairlady Z (Z33) | NISMO | 1:53.9290 |
| 37 | Tatsuya Kataoka / Sakon Yamamoto | Toyota Supra (JZA80) | Toyota Team Tom's | 1:54.2160 |
| 32 | Andre Lotterer / Tsugio Matsuda | Honda NSX (LA-NA2) | Nakajima Racing | 1:54.3080 |
| 100 | Sébastien Philippe / Jeremie Dufour | Honda NSX (LA-NA2) | Team Kunimitsu | 1:54.5470 |
| 35 | Peter Dumbreck / Naoki Hattori | Toyota Supra (JZA80) | KRAFT | 1:54.6310 |
| 38 | Toranosuke Takagi / Yuuji Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:54.7690 |
| 39 | André Couto / Ronnie Quintarelli | Toyota Supra (JZA80) | Toyota Team SARD | 1:54.8900 |
| 6 | Akira Iida / Juichi Wakisaka | Toyota Supra (JZA80) | Esso Toyota Team Le Mans | 1:54.9670 |
| 36 | James Courtney / Takeshi Tsuchiya / *Hideki Noda | Toyota Supra (JZA80) | Toyota Team Tom's | 1:55.2790 |
| 34 | Naoki Yokomizo / Seiji Ara | Toyota Supra (JZA80) | KRAFT | 1:57.6760 |
| 0 | Haruki Kurosawa / Shin'ya Hosokawa | Honda NSX (LA-NA2) | M-Tec Co.Ltd. | 2:01.5530 |
| 21 | Takuya Kurosawa / Hidetoshi Mitsusada | Ferrari 550 Maranello GTS | Hitotsuyama Racing | 2:01.6230 |
| 46 | Kazuki Hoshino / Takayuki Aoki | Nissan Fairlady Z (Z33) | Mola | 2:01.6910 |
| 11 | Tetsuya Tanaka / Paolo Montin | Ferrari 360 Modena (GF-F360) | Jim Gainer | 2:01.8150 |
| 30 | Kota Sasaki / Tetsuya Yamano | Toyota MR-S (GH-ZZW30) | Team Reckless | 2:02.0690 |
| 10 | Hideshi Matsuda / Yasutaka Hinoi | Ferrari 360 Modena (GF-F360) | Jim Gainer | 2:02.2630 |
| 19 | Nobuteru Taniguchi / Hiroki Katou | Toyota Celica (ZZT231) | Racing Project Bandoh | 2:03.1250 |
| 31 | Minoru Tanaka / Kazuki Nakajima | Toyota MR-S (GH-ZZW30) | Kicchouhouzan With Apr | 2:03.2540 |
| 13 | Mitsuhiro Kinoshita / Masami Kageyama | Nissan Fairlady Z (Z33) | Endless Sports | 2:03.6890 |
| 62 | Tadao Uematsu / Hiroyuki Yagi | Vemac RD350R | Willcom R&D Sport | 2:03.9170 |
| 7 | Shin'ichi Yamaji / Hiroyuki Iiri | Mazda RX-7 (FD3S) | RE Amemiya Racing | 2:04.5240 |
| 27 | Hiroki Yoshimoto / Shogo Mitsuyama | Vemac RD320R | Direxiv Motorsports | 2:05.1080 |
| 43 | Morio Nitta / Shinichi Takagi | ASL Garaiya (SA9VGR) | Autobacs Racing Team Aguri | 2:05.4200 |
| 112 | Atsushi Yogou / Takaya Tsubobayashi | Porsche 996 GT3 | Arktech Motorsports | 2:05.7570 |
| 52 | Hironori Takeuchi / Katsuyuki Hiranaka | Toyota Celica (ZZT231) | Toyota Team Cerumo | 2:06.6980 |
| 47 | Gou Shimizu / Tomonobu Fujii | Nissan Fairlady Z (Z33) | Mola | 2:06.7150 |
| 77 | Katsuo Kobayashi / Tatsuya Tanigawa | Subaru Impreza (GDB) | Cusco Racing | 2:06.8530 |
| 2 | Akira Watanabe / Kazuho Takahashi | Vemac RD320R | Verno Tokai Dream28 | 2:08.0930 |
| 110 | Ichijou Suga / Takashi Ooi | Porsche 986 Boxster | Arktech Motorsports | 2:08.2660 |
| 5 | Tetsuji Tamanaka / Katsuhiko Tsutsui | Vemac RD320R | Team Mach | 2:08.5120 |