| 1 | Ukyou Katayama / Toshio Suzuki / Keiichi Tsuchiya | Toyota GT-One (TS020) | Toyota Motorsports | 1:16.3490 |
| 23 | Erik Comas / Satoshi Motoyama / Masami Kageyama | Nissan R391 | NISMO | 1:16.8140 |
| 61 | Hiroki Katou / Juichi Wakisaka | BMW V12 LM | Team Goh/Dome | 1:18.9410 |
| 24 | Yojiro Terada / Franck Fréon / Kaichi Satou | Autoexe LMP99 Ford | Autoexe Motorsports | 1:22.1760 |
| 35 | Pierre-Henri Raphanel / Shin'ichi Yamaji / Takeshi Tsuchiya | Toyota Supra (JZA80) | Matsumotokiyoshi Team Tom's | 1:25.0740 |
| 32 | Takayuki Kinoshita / Masahiko Kondou / Hironori Takeuchi | Toyota Supra (JZA80) | cdma One Toyota Team Cerumo With Key's | 1:25.7490 |
| 6 | Hideki Noda / Wayne Gardner | Toyota Supra (JZA80) | Team Le Mans | 1:26.4410 |
| 21 | Akira Iida / Yasushi Hitotsuyama / Mikio Hitotsuyama | McLaren F1 GTR (S70) | Hitotsuyama Racing | 1:26.6550 |
| 11 | Takao Wada / Mitsuhiro Kinoshita / Yasushi Kikuchi | Nissan Skyline GT-R (BCNR33) | Endless Sports | 1:27.5810 |
| 56 | Vincent Vosse / Xavier Pompidou | Chrysler Viper GTS-R | Chamberlain Motorsport | 1:28.4830 |
| 15 | Wolfgang Kaufmann / Bob Wollek | Porsche 911 GT2 (993 GT2) | Freisinger Motorsport | 1:29.5270 |
| 60 | Seiji Ara / Hideki Okada | Chrysler Viper GTS-R | Team Goh/Chamberlain Engineering | 1:30.1000 |
| 28 | Kazuyuki Nishizawa / Takuya Kurosawa / Peter Dumbreck | Porsche 993 Carrera RSR | Tomei Sport | 1:31.1440 |
| 17 | Katsunori Iketani / Hiroyuki Nodi | Porsche 911 GT2 (993 GT2) | Freisinger Motorsport | 1:31.1680 |
| 64 | Stéphane Ortelli / Hisashi Wada | Porsche 911 GT2 (993 GT2) | Roock Sport System/Japan | 1:31.1680 |
| 81 | Hideshi Matsuda / Dominik Schwager | Porsche 996 GT3-R | Team Taisan Advan | 1:32.6640 |
| 16 | Yukihiro Hane / Ernst Palmberger | Porsche 911 GT2 (993 GT2) | Freisinger Motorsport | 1:32.7850 |
| 69 | Gerold Ried / Christian Ried / Manfred Jurasz | Porsche 911 GT2 (993 GT2) | Proton Competition | 1:34.4570 |
| 70 | Yoshimi Ishibashi / Patrick van Schoote / Jun Harada | Porsche 911 GT2 (993 GT2) | Team Gaikokuya | 1:36.8970 |
| 65 | Manabu Orido / Takashi Suzuki / Tomiko Yoshikawa | Porsche 993 Carrera RSR | Roock Sport System/Japan | 1:39.7780 |
| 10 | Hidehiko Asou / Yasutaka Hinoi / Atsushi Yogou | Porsche 911 GT2 (993 GT2) | Ability Motorsports | 1:40.6700 |
| 91 | Masamitsu Ishihara / Kiichi Takahashi / Tomohiko Sunako | Porsche 993 Carrera RSR | 910 Racing | 2:25.6960 |