| Pos. |
No. |
Rider |
Type |
Time |
Delay |
Gap |
Lap |
Team |
| 1 | 75 | Seiji Osaki | YZF-R6 | 1'56.510 | 148.36km/h | | 7/7 | Ito Racing GMP Suzuka |
| 2 | 3 | Kazuma Watanabe | CBR600RR | 1'56.629 | 0.119 | 0.119 | 8/8 | KoharaRacing |
| 3 | 43 | Nobutomi Shinichi | YZF-R6 | 1'56.645 | 0.135 | 0.016 | 7/8 | HiTMAN RC Koshien Yamaha |
| 4 | 30 | DECHA KRAISART | YZF-R6 | 1'56.761 | 0.251 | 0.116 | 4/8 | Yamaha Thailand Racing Team |
| 5 | 634 | Ryuta Kobayashi | CBR600RR | 1'57.123 | 0.613 | 0.362 | 4/8 | MuSASHi RT HULKPRO |
| 6 | 16 | Hiro Michi Kunigawa | CBR600RR | 1'57.126 | 0.616 | 0.003 | 7/7 | HiRaNo・HouYou |
| 7 | 62 | Ryuji Yoko | YZF R-6 | 1'57.293 | 0.783 | 0.167 | 7/8 | RT Bear in the Forest Sato School |
| 8 | 52 | Zamri Baba | YZF-R6 | 1'57.342 | 0.832 | 0.049 | 7/8 | PETRONAS-YAMAHA-Malaysia/41PLAN |
| 9 | 65 | CHALERMPOL POLAMAI | YZF-R6 | 1'57.469 | 0.959 | 0.127 | 6/8 | Yamaha Thailand Racing Team |
| 10 | 6 | Yuji Sato | YZF-R6 | 1'57.518 | 1.008 | 0.049 | 6/8 | HiTMAN RC Koshien Yamaha |
| 11 | 15 | Takuya Tsuda | GSX-R600 | 1'57.633 | 1.123 | 0.115 | 7/8 | WestPower |
| 12 | 77 | Jin Yasushi Izutsu | ZX-6R | 1'57.885 | 1.375 | 0.252 | 6/8 | RS-ITOH & ASIA |
| 13 | 19 | Yuki Ito | YZF-R6 | 1'57.888 | 1.378 | 0.003 | 7/7 | DOG FIGHT RACING - YAMAHA |
| 14 | 37 | Yuuya Kondo | YZF-R6 | 1'59.011 | 2.501 | 1.123 | 3/6 | GBS Racing |
| 15 | 20 | Shintaro Nakayama | CBR600RR | 1'59.197 | 2.687 | 0.186 | 5/8 | TEAM Shintaro with KRT |
| 16 | 9 | Tetsuro Iwa | ZX-6R | 1'59.204 | 2.694 | 0.007 | 7/7 | RS-ITOH & ASIA |
| 17 | 12 | Mitsunori Okamura | CBR600RR | 1'59.334 | 2.824 | 0.130 | 7/8 | RSG Racing & Dream Kitakyushu |
| 18 | 17 | Makoto Inagaki | YZF-R6 | 1'59.454 | 2.944 | 0.120 | 4/7 | Akeno Speed MIC |
| 19 | 56 | Akutsu Koki | YZF-R6 | 1'59.485 | 2.975 | 0.031 | 7/8 | DOG FIGHT RACING - YAMAHA |
| 20 | 28 | Shota Fujishima | CBR600RR | 1'59.714 | 3.204 | 0.229 | 4/8 | 4Sure Honda Dream Nagoya West |
| 21 | 46 | Shigenobu Oda | GSX-R600 | 1'59.769 | 3.259 | 0.055 | 4/7 | Evolution Spirit & Ojaz Factory |
| 22 | 23 | Yusuke Tejima | CBR600RR | 2'00.155 | 3.645 | 0.386 | 4/6 | CLUB PLUS ONE |
| 23 | 25 | Naoki Shimizu | YZF-R6 | 2'00.256 | 3.746 | 0.101 | 6/7 | Express Houyou |
| 24 | 67 | Akihiro Iota | ZX-6R | 2'00.424 | 3.914 | 0.168 | 7/7 | RS-ITOH |
| 25 | 54 | Shuichi Nagashima | CBR600RR | 2'01.006 | 4.496 | 0.582 | 3/5 | Ishii Apple Orchard Moto Alpha |
| 26 | 53 | Naohiro Nakatsuhara | CBR600RR | 2'01.030 | 4.520 | 0.024 | 5/6 | Kenyuukai Tochigi PG Racing |
| 27 | 44 | Yasuhiro Matsukawa | CBR600RR | 2'01.129 | 4.619 | 0.099 | 3/7 | MOTO BUM HONDA |
| 28 | 32 | Takuma Fukatsu | CBR600RR | 2'01.166 | 4.656 | 0.037 | 6/7 | Team Sugai Racing Japan |
| 29 | 26 | Sasuke Shinozaki | YZF-R6 | 2'01.179 | 4.669 | 0.013 | 4/6 | SP Tadao Racing Team |
| 30 | 55 | Naoki Hasegawa | SX-R600L1 | 2'02.607 | 6.097 | 1.428 | 3/6 | CONFIA-HMF & AS Ogasawara |
| 31 | 72 | Tomohiro Nakayama | CBR600RR | 2'03.155 | 6.645 | 0.548 | 4/6 | MCR Garage Orange Works |
| 32 | 57 | Toyohiro Nakamura | CBR600RR | 2'03.177 | 6.667 | 0.022 | 7/8 | Acro Racing + Moto Bump |
| 33 | 64 | Eiichiro Yada | YZF-R6 | 2'03.193 | 6.683 | 0.016 | 5/8 | T.T.MOTO |
| 34 | 58 | Taku Obara | CBR600RR | 2'03.680 | 7.170 | 0.487 | 7/7 | MCR Garage Orange Works |
| 35 | 47 | Riki Suzuki | CBR600RR | 2'04.235 | 7.725 | 0.555 | 5/7 | CLUB HARC-PRO. |