| Pos | No. | Name | Time | Delay | Gap | Lap | Type | Team | ||
| 1 | 9 | Katsuyuki Nakasuga | 1'51.805 | 154.60Km/h | 6/16 | YZF-R1 | YSP&PRESTO Racing | |||
| 2 | 3 | Tatsuya Yamaguchi | 1'51.848 | 0.043 | 0.043 | 9/14 | CBR1000RR | Moriwaki MOTUL Racing | ||
| 3 | 83 | Naoya Moriwaki | 1'52.028 | 0.223 | 0.180 | 16/18 | CBR1000RR | Moriwaki MOTUL Racing | ||
| 4 | 87 | Yanagawa Akira | 1'52.407 | 0.602 | 0.379 | 12/16 | ZX-10R | TEAM GREEN | ||
| 5 | 81 | Noriaki Abe | 1'52.481 | 0.676 | 0.074 | 7/7 | YZF-R1 | Wise Gear Racing | ||
| 6 | 54 | Tokudome Kazuki | 1'52.493 | 0.688 | 0.012 | 14/18 | CBR1000RR | Honda Dream Infinity RT | ||
| 7 | 76 | Atsushi Watanabe | 1'52.735 | 0.930 | 0.242 | 13/19 | GSX-R1000 | Yoshimura Suzuki with JOMO | ||
| 8 | 39 | Sakai Daisaku | 1'52.957 | 1.152 | 0.222 | 19/20 | GSX-R1000 | Yoshimura Suzuki with JOMO | ||
| 9 | 10 | Kameya Nagajun | 1'52.959 | 1.154 | 0.002 | 5/5 | CBR1000RR | Team Sakurai Honda | ||
| 10 | 4 | Kosuke Akiyoshi | 1'52.963 | 1.158 | 0.004 | 15/16 | GSX-R1000K7 | WINs SUZUKI R.T | ||
| 11 | 75 | Makoto Osaki | 1'53.439 | 1.634 | 0.476 | 4/5 | YZF-R1 | SP Tadao Racing Team | ||
| 12 | 73 | Yasuda Takeshi | 1'53.441 | 1.636 | 0.002 | 15/15 | CBR1000RR | team HARC-PRO. | ||
| 13 | 7 | Tsujimura Takeshi | 1'53.625 | 1.820 | 0.184 | 11/14 | CBR1000RR | F.C.C.TSR | ||
| 14 | 48 | Yusuke Teshima | 1'53.678 | 1.873 | 0.053 | 12/15 | CBR1000RR | TEAM HRC | ||
| 15 | 6 | Exit Repair | 1'54.252 | 2.447 | 0.574 | 15/15 | CBR1000RR | Team OSG & Motorsports | ||
| 16 | 30 | Yuki Hatano | 1'54.500 | 2.695 | 0.248 | 15/17 | GSX-R1000K7 | Moto Map SUPPLY | ||
| 17 | 53 | Yukihisa Konno | 1'54.840 | 3.035 | 0.340 | 8/11 | GSX-R1000K7 | Deotex PANTHERA | ||
| 18 | 11 | Yoshiyuki Sugai | 1'54.879 | 3.074 | 0.039 | 12/18 | CBR1000RR | KEIHINKoharaR.T. | ||
| 19 | 71 | Kazuma Tsuda | 1'55.219 | 3.414 | 0.340 | 19/20 | CBR1000RR | Team Sakurai Honda | ||
| 20 | 17 | Masayuki Yamanaka | 1'55.746 | 3.941 | 0.527 | 12/15 | CBR1000RR | Tele'Wolfman Yoshiharu MCR | ||
| 21 | 16 | Yoshimasa Kawase | 1'55.749 | 3.944 | 0.003 | 17/17 | GSX-R1000K7 | WINs SUZUKI R.T | ||
| 22 | 23 | Koji Honda | 1'56.199 | 4.394 | 0.450 | 4/6 | GSX-R1000K7 | Marumae Racing Supply | ||
| 23 | 24 | Kanda Shouhei | 1'56.247 | 4.442 | 0.048 | 7/13 | ZX-10R | RS-ITOH&KAZE | ||
| 24 | 33 | Hideki Matsui | 1'57.223 | 5.418 | 0.976 | 15/18 | CBR1000RR | BATTLE&Mihara Racing | ||
| 25 | 32 | Hayato Takada | 1'57.364 | 5.559 | 0.141 | 13/15 | CBR1000RR | TEAM D Kanto Matsudo R& Toriko | ||
| 26 | 704 | Tomoya Nakamura | 1'57.446 | 5.641 | 0.082 | 18/18 | CBR1000RR | Meiwa Racing | ||
| 27 | 85 | Katsuyoshi Furukawa | 1'57.948 | 6.143 | 0.502 | 14/17 | CBR1000RR | Honda Hamatomo Club Hamamatsu Escargot | ||
| 28 | 37 | Shinya Harada | 1'57.993 | 6.188 | 0.045 | 5/18 | CBR1000RR | TEAM D Kanto Funabashi R& Toriko | ||
| 29 | 35 | Atsuyuki Kobayashi | 1'58.449 | 6.644 | 0.456 | 6/6 | CBR1000RR | Honda Blue Helmet MSC | ||
| 30 | 21 | Shinji Noyori | 1'58.875 | 7.070 | 0.426 | 5/16 | CBR1000RR | Honda Hamatomo Club Hamamatsu Escargot | ||
| 31 | 70 | Hideyoshi Yoshii | 1'59.298 | 7.493 | 0.423 | 10/17 | GSX-R1000 | Fukushima Ophthalmology Clinic teamJUNBO | ||
| Above qualifying vehicles: (Official qualifying 2nd run available) | ||||||||||
| 32 | 36 | Naoki Yamada | 1'59.924 | 8.119 | 0.626 | 14/16 | GSX-R1000K7 | TEAM Z-TECH | ||
| 33 | 93 | Takaharu Masayuki | 2'00.420 | 8.615 | 0.496 | 13/15 | YZF-R1 | EISHIN Racing | ||
| 34 | 68 | Samurai Exhibition Photo | 2'00.781 | 8.976 | 0.361 | 4/12 | GSX-R1000 | Compus・OUTRUN | ||
| 35 | 38 | Hiroshi Harada | 2'00.983 | 9.178 | 0.202 | 9/17 | ZX1000D6F | R.S. Garage Harada Himeji | ||
| 36 | 34 | Yosuke Washimi | 2'01.454 | 9.649 | 0.471 | 12/15 | GSX-R1000 | TEAM Z-TECH | ||
| 37 | 77 | Kanayama Kazuhiro | 2'02.232 | 10.427 | 0.778 | 4/16 | GSX-R1000 | Team Hashimoto Group - Sakura | ||
| 38 | 47 | Takahide Goto | Unable to measure | YZF-R1 | GBS Racing Garage Hoshi | |||||