(All Session Laps)
| Pos. | No. | Drivers | Car | Entrant | All Best | Q Time | FL Time |
| 1st | 18 | Wakisaka / Kaneishi | Honda NSX (GH-NA2) | Dome Mugen Project | 1:20.296 | 1:20.2960 | |
| 2nd | 64 | Itou / Schwager | Honda NSX (GH-NA2) | Mobil1 Nakajima Racing | 1:20.581 | 1:20.5810 | 1:22.2100 |
| 3rd | 36 | Sekiya / Tsuchiya | Toyota Supra (JZA80) | Toyota Castrol Team Tom's | 1:20.713 | 1:20.7130 | |
| 4th | 6 | Noda / Gardner | Toyota Supra (JZA80) | Esso Ultron Toyota Team Le Mans | 1:20.735 | 1:20.7350 | |
| 5th | 16 | Nakako / Michigami | Honda NSX (GH-NA2) | Dome Mugen Project | 1:20.763 | 1:20.7630 | |
| 6th | 21 | Hitotsuyama / Nakaya | McLaren F1 GTR | Hitotsuyama Racing | 1:20.889 | 1:20.8890 | |
| 7th | 37 | Ara / Suzuki | Toyota Supra (JZA80) | Toyota Castrol Team Tom's | 1:21.178 | 1:21.1780 | |
| 8th | 35 | Yamaji / Raphanel | Toyota Supra (JZA80) | Matsumotokiyoshi Team Tom's | 1:21.249 | 1:21.2490 | |
| 9th | 100 | Iida / Hattori | Honda NSX (GH-NA2) | Team Kunimitsu With Mooncraft | 1:21.253 | 1:21.2530 | |
| 10th | 2 | Katayama / Krumm | Nissan Skyline GT-R (BNR34) | NISMO | 1:21.291 | 1:21.2910 | |
| 11th | 39 | Kageyama / Firman | Toyota Supra (JZA80) | Toyota Team SARD | 1:21.360 | 1:21.3600 | |
| 12th | 12 | Hoshino / Motoyama | Nissan Skyline GT-R (BNR34) | Team Impul | 1:21.387 | 1:21.3870 | |
| 13th | 8 | Suzuki / Tsuchiya | Honda NSX (E-NA2) | Autobacs Racing Team Aguri | 1:21.416 | 1:21.4160 | |
| 14th | 38 | Takeuchi / Tachikawa | Toyota Supra (JZA80) | Toyota Team Cerumo | 1:21.457 | 1:21.4570 | |
| 15th | 1 | Comas / Kageyama | Nissan Skyline GT-R (BNR34) | NISMO | 1:21.661 | 1:21.6610 | |
| 16th | 30 | Yamada / Okada | McLaren F1 GTR | Team Take One | 1:21.945 | 1:21.9450 | |
| 17th | 25 | Kinoshita / Orido | Toyota Supra (JZA80) | Endless+Tsuchiya Engineering | 1:21.946 | 1:21.9460 | |
| 18th | 3 | Hasemi / Tanaka | Nissan Skyline GT-R (BNR34) | Hasemi Motorsports | 1:22.361 | 1:22.3610 | |
| 19th | 32 | Kinoshita / Kondou | Toyota Supra (JZA80) | cdma One Toyota Team Cerumo With Key's | 1:22.374 | 1:22.3740 | |
| 20th | 88 | Furuya / Takahashi | Lamborghini Diablo (ZA90DE068) | JLOC | 1:23.052 | 1:23.0520 | |
| 21st | 7 | Matsumoto / Yamano | Mazda RX-7 (FD3S) | RE Amemiya Racing | 1:27.272 | 1:27.2720 | 2:28.8000 |
| 22nd | 26 | Fukuyama / Mizuno | Porsche 996 GT3-R | Team Taisan Jr. With Advan | 1:28.189 | 1:28.1890 | |
| 23rd | 910 | Yogou / Wada | Porsche 996 GT3-R | 910 Racing | 1:28.306 | 1:28.3060 | |
| 24th | 81 | Ohyagi / Aoki | Nissan Silvia (S15) | Team Daishin | 1:28.403 | 1:28.4030 | |
| 25th | 86 | Tanaka / Matsuda | Toyota Trueno (AE86) | Kraft | 1:28.549 | 1:28.5490 | |
| 26th | 19 | Wakisaka / Hara | Toyota Celica (ST205) | Racing Project Bandoh | 1:28.559 | 1:28.5590 | |
| 27th | 31 | Nitta / Igarashi | Toyota MR-S (GH-ZZW30) | Super Autobacs A'pex MR-S | 1:28.568 | 1:28.5680 | |
| 28th | 10 | Hinoi / Yamagishi | Porsche 911 GT2 | Ability Motorsports | 1:29.042 | 1:29.0420 | |
| 29th | 911 | Ishihara / Sunako | Porsche 996 GT3-R | 910 Racing | 1:29.152 | 1:29.1520 | |
| 30th | 77 | Kobayashi / Tanigawa | Subaru Impreza (GC4) | Cusco Racing | 1:29.269 | 1:29.2690 | |
| 31st | 71 | Jounai / Kawano | Porsche 911 GT2 | Sigmatech Racing Team | 1:29.767 | 1:29.7670 | |
| 32nd | 28 | Suga / Shibahara | Porsche 996 GT3-R | Team Taisan Jr. With Advan | 1:29.822 | 1:29.8220 | |
| 33rd | 69 | Malagamuwa / Tamamoto | Mirage GT1 Chevrolet | Team Sri Lanka | 1:29.916 | 1:29.9160 | |
| 34th | 51 | Sodeyama / Yamada | Nissan Silvia (S14) | Auto Staff Racing Team | 1:30.191 | 1:30.1910 | |
| 35th | 24 | Nishizawa / Apicella | Porsche 986 Boxster | MTCI Racing Team | 1:30.814 | 1:30.8140 | |
| 36th | 70 | Ishibashi / Komiya | Porsche 911 GT2 | Team Gaikokuya | 1:30.970 | 1:30.9700 | |
Entered cars that did not arrive:
| No. | Drivers | Car | Entrant |
| 55 | Suga / Shibahara | Chrysler Viper GTS-R | Team Taisan |
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