| Pos | No. | Name | Time | Delay | Gap | Lap | Type | Team | ||
| 1 | 25 | Toshio Higashiura | 1'56.962 | 147.78Km/h | 9/9 | YZF-R6 | Plus Mue Racing Team | |||
| 2 | 5 | Koji Teramoto | 1'57.614 | 0.652 | 0.652 | 5/14 | GSX-R600K7 | Moto Map VEGA | ||
| 3 | 88 | Yuichi Takeda | 1'57.679 | 0.717 | 0.065 | 5/15 | CBR600RR | Team Sakurai Honda | ||
| 4 | 73 | Ryoki Konishi | 1'57.688 | 0.726 | 0.009 | 4/14 | CBR600RR | team HARC-PRO. | ||
| 5 | 6 | Okuno Masao | 1'57.860 | 0.898 | 0.172 | 12/15 | YZF-R6 | Ito RACING · GMD Suzuka | ||
| 6 | 55 | Eiki Takahashi | 1'58.056 | 1.094 | 0.196 | 6/16 | CBR600RR | DyDo MiU Racing | ||
| 7 | 12 | Hiroki Noda | 1'58.072 | 1.110 | 0.016 | 14/15 | CBR600RR | Racing Team Honeybee | ||
| 8 | 705 | Takehiko Kurokawa | 1'58.125 | 1.163 | 0.053 | 8/12 | CBR600RR | GARAGESPEED Nakamura Eg | ||
| 9 | 10 | Yuuji Sato | 1'58.164 | 1.202 | 0.039 | 4/4 | YZF-R6 | Jubilo Racing Team | ||
| 10 | 16 | Masahiko Oishi | 1'58.172 | 1.210 | 0.008 | 11/13 | YZF-R6 | Ito RACING · GMD Suzuka | ||
| 11 | 8 | Takahashi Hidekuni | 1'58.257 | 1.295 | 0.085 | 6/13 | ZX-6R | TEAM GREEN | ||
| 12 | 45 | Michio Izumi | 1'58.383 | 1.421 | 0.126 | 10/14 | CBR600RR | Honda Dream Kitakyushu RT | ||
| 13 | 72 | Atsushi Miyazaki | 1'58.474 | 1.512 | 0.091 | 13/13 | YZF-R6 | DOG FIGHT RACING | ||
| 14 | 15 | Makoto Inagaki | 1'58.510 | 1.548 | 0.036 | 5/12 | CBR600RR | Burning Blood RT | ||
| 15 | 43 | Hideyuki Ikata | 1'58.544 | 1.582 | 0.034 | 5/13 | GSX-R600 | Espal's Dream Racing | ||
| 16 | 58 | Takayuki Oki | 1'58.596 | 1.634 | 0.052 | 16/17 | CBR600RR | Club HARC-PRO. | ||
| 17 | 20 | Satoru Iwata | 1'58.632 | 1.670 | 0.036 | 14/17 | CBR600RR | F.C.C.TSR | ||
| 18 | 17 | Toshiyuki Aragaki | 1'58.827 | 1.865 | 0.195 | 11/14 | CBR600RR | Team ARA Tiger's Den | ||
| 19 | 51 | Masahiro Izumimoto | 1'58.852 | 1.890 | 0.025 | 13/15 | YZF-R6 | RT Mori no Kumasan Sato Juku Sendai | ||
| 20 | 54 | Tetsugo Inoue | 1'59.077 | 2.115 | 0.225 | 12/17 | ZX-6R | TrickStar Tamiton-R | ||
| 21 | 11 | Mori Shin | 1'59.177 | 2.215 | 0.100 | 12/16 | CBR600RR | team HARC-PRO. | ||
| 22 | 44 | Yuta Kodama | 1'59.245 | 2.283 | 0.068 | 11/15 | CBR600RR | DDBOYS Racing | ||
| 23 | 37 | Yukari Tomoki | 1'59.453 | 2.491 | 0.208 | 17/17 | GSX-R600 | Yoshimura Suzuki with JOMO | ||
| 24 | 27 | Masataro Nakayama | 1'59.523 | 2.561 | 0.070 | 4/14 | CBR600RR | Kohara RC | ||
| 25 | 89 | Suma Sadahito | 1'59.617 | 2.655 | 0.094 | 5/15 | CBR600RR | Honda Dream Kitakyushu RT | ||
| 26 | 76 | Naoki Shimizu | 1'59.624 | 2.662 | 0.007 | 11/11 | ZX-6R | RS-ITOH&KAZE | ||
| 27 | 23 | Norimori Numata | 1'59.669 | 2.707 | 0.045 | 5/16 | YZF-R6 | HITMAN RC Motegi Yamaha | ||
| 28 | 56 | Takashi Harada | 1'59.768 | 2.806 | 0.099 | 12/13 | CBR600RR | CLUB HARC-PRO. | ||
| 29 | 34 | Hidefumi Kawahara | 1'59.791 | 2.829 | 0.023 | 15/15 | CBR600RR | TEAM PLUS ONE | ||
| 30 | 29 | Takuya Tsuda | 1'59.839 | 2.877 | 0.048 | 10/16 | CBR600RR | Team OSG & Motorsports | ||
| 31 | 62 | Nakahara Naohiro | 1'59.841 | 2.879 | 0.002 | 12/16 | CBR600RR | Tochigi PG Racing Club | ||
| 32 | 85 | Daisuke Nakajima | 1'59.916 | 2.954 | 0.075 | 14/15 | ZX-6R | MAX-SPEED | ||
| 33 | 28 | Yukimi Shimizu | 2'00.044 | 3.082 | 0.128 | 10/15 | CBR600RR | DREAM Takasaki B'WISE RT | ||
| 34 | 69 | Ryuta Kobayashi | 2'00.257 | 3.295 | 0.213 | 15/15 | CBR600RR | Burning Blood RT | ||
| 35 | 65 | Mt. Kosuge | 2'00.274 | 3.312 | 0.017 | 15/15 | CBR600RR | CLUB HARC-PRO. | ||
| 36 | 99 | Naoko Takasugi | 2'00.464 | 3.502 | 0.190 | 10/17 | CBR600RR | Racing Team Honeybee | ||
| 37 | 33 | Shimochi Shingo | 2'00.544 | 3.582 | 0.080 | 11/15 | ZX-6RR | Ambitious Panasonic LUMIX | ||
| 38 | 60 | Hiroshi Furuhata | 2'01.007 | 4.045 | 0.463 | 12/15 | CBR600RR | R.T Honeybee Matsuda Juku | ||
| 39 | 57 | Yokobari Kōkaku | 2'01.026 | 4.064 | 0.019 | 15/16 | GSX-R600 | SBS Iwata | ||
| 40 | 63 | Yoshihiro Kishimoto | 2'01.472 | 4.510 | 0.446 | 5/17 | CBR600RR | Yokohama F. Marinos & Ozawa R&D + Matsuda Juku | ||
| 41 | 83 | Terao Ono | 2'01.612 | 4.650 | 0.140 | 15/16 | GSX-R600 | SBS Aizu Light On | ||
| 42 | 77 | Shonosuke Oda | 2'01.869 | 4.907 | 0.257 | 6/6 | CBR600RR | Honda Shop Nagano R·T | ||
| 43 | 59 | Takakazu Akabane | 2'03.026 | 6.064 | 1.157 | 12/15 | CBR600RR | |||
| 44 | 38 | Yoshikazu Yasumi | 2'03.097 | 6.135 | 0.071 | 5/14 | YZF-R6 | DOG FIGHT RACING | ||
| 45 | 91 | Daniel Silva | 2'03.870 | 6.908 | 0.773 | 10/16 | GSX-R600K6 | Kentsu J Trust Racing | ||
| 19 | Tatsuo Tsuruta | Did not participate | ZX-6R | TrickStar Tamiton-R | ||||||
| 61 | Yasutaka Kojima | Did not participate | CBR600RR | MC Racing |