| Pos | No. | Name | Time | Delay | Gap | Lap | Type | Team | ||
| 1 | 72 | Atsushi Miyazaki | 2'01.413 | 142.37Km/h | 6/6 | YZF-R6 | DOG FIGHT RACING | |||
| 2 | 12 | Hiroki Noda | 2'02.947 | 1.534 | 1.534 | 6/6 | CBR600RR | Racing Team Honeybee | ||
| 3 | 23 | Norimori Numata | 2'03.111 | 1.698 | 0.164 | 5/5 | YZF-R6 | HITMAN RC Motegi Yamaha | ||
| 4 | 44 | Yuta Kodama | 2'03.143 | 1.730 | 0.032 | 6/6 | CBR600RR | DDBOYS Racing | ||
| 5 | 43 | Hideyuki Ikata | 2'03.211 | 1.798 | 0.068 | 6/6 | GSX-R600 | Espal's Dream Racing | ||
| 6 | 62 | Nakahara Naohiro | 2'03.404 | 1.991 | 0.193 | 7/7 | CBR600RR | Tochigi PG Racing Club | ||
| 7 | 88 | Yuichi Takeda | 2'03.514 | 2.101 | 0.110 | 7/7 | CBR600RR | Team Sakurai Honda | ||
| 8 | 76 | Naoki Shimizu | 2'03.755 | 2.342 | 0.241 | 6/6 | ZX-6R | RS-ITOH&KAZE | ||
| 9 | 73 | Ryoki Konishi | 2'03.904 | 2.491 | 0.149 | 6/6 | CBR600RR | team HARC-PRO. | ||
| 10 | 28 | Yukimi Shimizu | 2'04.028 | 2.615 | 0.124 | 7/7 | CBR600RR | DREAM Takasaki B'WISE RT | ||
| 11 | 27 | Masataro Nakayama | 2'04.119 | 2.706 | 0.091 | 6/6 | CBR600RR | Kohara RC | ||
| 12 | 60 | Hiroshi Furuhata | 2'04.503 | 3.090 | 0.384 | 4/4 | CBR600RR | R.T Honeybee Matsuda Juku | ||
| 13 | 55 | Eiki Takahashi | 2'04.609 | 3.196 | 0.106 | 5/5 | CBR600RR | DyDo MiU Racing | ||
| 14 | 8 | Takahashi Hidekuni | 2'04.906 | 3.493 | 0.297 | 6/6 | ZX-6R | TEAM GREEN | ||
| 15 | 45 | Michio Izumi | 2'05.263 | 3.850 | 0.357 | 5/5 | CBR600RR | Honda Dream Kitakyushu RT | ||
| 16 | 16 | Masahiko Oishi | 2'05.583 | 4.170 | 0.320 | 6/6 | YZF-R6 | Ito RACING · GMD Suzuka | ||
| 17 | 99 | Naoko Takasugi | 2'05.616 | 4.203 | 0.033 | 6/6 | CBR600RR | Racing Team Honeybee | ||
| 18 | 37 | Yukari Tomoki | 2'05.783 | 4.370 | 0.167 | 7/7 | GSX-R600 | Yoshimura Suzuki with JOMO | ||
| 19 | 51 | Masahiro Izumimoto | 2'06.058 | 4.645 | 0.275 | 5/5 | YZF-R6 | RT Mori no Kumasan Sato Juku Sendai | ||
| 20 | 5 | Koji Teramoto | 2'06.276 | 4.863 | 0.218 | 5/5 | GSX-R600K7 | Moto Map VEGA | ||
| 21 | 89 | Suma Sadahito | 2'06.454 | 5.041 | 0.178 | 7/7 | CBR600RR | Honda Dream Kitakyushu RT | ||
| 22 | 15 | Makoto Inagaki | 2'06.843 | 5.430 | 0.389 | 3/3 | CBR600RR | Burning Blood RT | ||
| 23 | 57 | Yokobari Kōkaku | 2'06.960 | 5.547 | 0.117 | 7/7 | GSX-R600 | SBS Iwata | ||
| 24 | 20 | Satoru Iwata | 2'07.250 | 5.837 | 0.290 | 4/4 | CBR600RR | F.C.C.TSR | ||
| 25 | 10 | Yuuji Sato | 2'07.561 | 6.148 | 0.311 | 4/6 | YZF-R6 | Jubilo Racing Team | ||
| 26 | 85 | Daisuke Nakajima | 2'07.904 | 6.491 | 0.343 | 4/4 | ZX-6R | MAX-SPEED | ||
| 27 | 17 | Toshiyuki Aragaki | 2'08.598 | 7.185 | 0.694 | 5/6 | CBR600RR | Team ARA Tiger's Den | ||
| 28 | 34 | Hidefumi Kawahara | 2'09.092 | 7.679 | 0.494 | 5/5 | CBR600RR | TEAM PLUS ONE | ||
| 29 | 29 | Takuya Tsuda | 2'09.153 | 7.740 | 0.061 | 6/6 | CBR600RR | Team OSG & Motorsports | ||
| 30 | 11 | Mori Shin | 2'09.554 | 8.141 | 0.401 | 6/6 | CBR600RR | team HARC-PRO. | ||
| 31 | 65 | Mt. Kosuge | 2'10.190 | 8.777 | 0.636 | 6/6 | CBR600RR | CLUB HARC-PRO. | ||
| 32 | 33 | Shimochi Shingo | 2'10.418 | 9.005 | 0.228 | 4/4 | ZX-6RR | Ambitious Panasonic LUMIX | ||
| 33 | 63 | Yoshihiro Kishimoto | 2'13.581 | 12.168 | 3.163 | 7/7 | CBR600RR | Yokohama F. Marinos & Ozawa R&D + Matsuda Juku | ||
| 34 | 6 | Okuno Masao | 2'15.537 | 14.124 | 1.956 | 3/6 | YZF-R6 | Ito RACING · GMD Suzuka | ||
| 35 | 705 | Takehiko Kurokawa | 2'16.243 | 14.830 | 0.706 | 2/4 | CBR600RR | GARAGESPEED Nakamura Eg | ||
| 36 | 58 | Takayuki Oki | 2'16.933 | 15.520 | 0.690 | 4/4 | CBR600RR | Club HARC-PRO. | ||
| 37 | 56 | Takashi Harada | 2'18.821 | 17.408 | 1.888 | 3/5 | CBR600RR | CLUB HARC-PRO. | ||
| 38 | 69 | Ryuta Kobayashi | 2'26.357 | 24.944 | 7.536 | 3/4 | CBR600RR | Burning Blood RT | ||
| 39 | 25 | Toshio Higashiura | 2'36.910 | 35.497 | 10.553 | 3/3 | YZF-R6 | Plus Mue Racing Team | ||
| 40 | 54 | Tetsugo Inoue | 3'01.659 | 1'00.246 | 24.749 | 2/2 | ZX-6R | TrickStar Tamiton-R |