| Pos | No. | Name | Time | Delay | Gap | Lap | Type | Car Name/Team | ||
| 1 | 10 | Kameya Nagajun | 2'01.478 | 142.29Km/h | June 7 | CBR1000RR | Team Sakurai Honda | |||
| 2 | 81 | Noriaki Abe | 2'02.225 | 0.747 | 0.747 | August 8 | YZF-R1 | Wise Gear Racing | ||
| 3 | 4 | Kosuke Akiyoshi | 2'02.349 | 0.871 | 0.124 | 7/7 | GSX-R1000K7 | WINs SUZUKI R.T | ||
| 4 | 83 | Naomori Moriwaki | 2'02.772 | 1.294 | 0.423 | 5/7 | CBR1000RR | Moriwaki MOTUL Racing | ||
| 5 | 87 | Yanagawa Akira | 2'03.004 | 1.526 | 0.232 | 5/7 | ZX-10R | TEAM GREEN | ||
| 6 | 76 | Atsushi Watanabe | 2'03.092 | 1.614 | 0.088 | 7/7 | GSX-R1000 | Yoshimura Suzuki with JOMO | ||
| 7 | 48 | Yusuke Teshima | 2'03.270 | 1.792 | 0.178 | 7/8 | CBR1000RR | TEAM HRC | ||
| 8 | 3 | Tatsuya Yamaguchi | 2'03.314 | 1.836 | 0.044 | 4/6 | CBR1000RR | Moriwaki MOTUL Racing | ||
| 9 | 39 | Sakai Daisaku | 2'04.118 | 2.640 | 0.804 | 7/7 | GSX-R1000 | Yoshimura Suzuki with JOMO | ||
| Above, decided in Round 3 session. | ||||||||||
| 10 | 54 | Tokudome Kazuki | 2'04.994 | 4/7 | CBR1000RR | Honda Dream Infinity RT | ||||
| 11 | 9 | Katsuyuki Nakasuga | 2'05.501 | 0.507 | 5/5 | YZF-R1 | YSP&PRESTO Racing | |||
| 12 | 73 | Yasuda Takeshi | 2'06.449 | 0.948 | June 7 | CBR1000RR | team HARC-PRO. | |||
| 13 | 75 | Makoto Osaki | 2'06.627 | 0.178 | 5/7 | YZF-R1 | SP Tadao Racing Team | |||
| 14 | 53 | Yukihisa Konno | 2'08.165 | 1.538 | 4/7 | GSX-R1000K7 | Deotex PANTHERA | |||
| 15 | 71 | Kazuma Tsuda | 2'08.491 | 0.326 | June 7 | CBR1000RR | Team Sakurai Honda | |||
| 16 | 32 | Hayato Takada | 2'08.807 | 0.316 | 5/6 | CBR1000RR | TEAM D Kanto Matsudo R& Toriko | |||
| 17 | 33 | Hideki Matsui | 2'09.210 | 0.403 | 5/5 | CBR1000RR | BATTLE & Mihara Racing | |||
| 18 | 11 | Yoshiyuki Sugai | 2'09.373 | 0.163 | 7/7 | CBR1000RR | KEIHINKoharaR.T. | |||
| 19 | 85 | Katsuyoshi Furukawa | 2'11.690 | 2.317 | 4/7 | CBR1000RR | Honda Hamatomo Club Hamamatsu Escargot | |||
| 20 | 7 | Tsujimura Takeshi | 2'12.862 | 1.172 | 3/3 | CBR1000RR | F.C.C.TSR | |||
| 21 | 17 | Masayuki Yamanaka | Did not participate | CBR1000RR | Tele'Wolfman Yoshiharu MCR | |||||
| Above, determined in Round 2 session. | ||||||||||
| 22 | 21 | Shinji Noyori | 2'12.161 | 7/7 | CBR1000RR | Honda Hamatomo Club Hamamatsu Escargot | ||||
| 23 | 23 | Koji Honda | 2'13.377 | 1.216 | June 6 | GSX-R1000K7 | Marumae Racing Supply | |||
| 24 | 24 | Kanda Shouhei | 2'14.320 | 0.943 | 7/7 | ZX-10R | RS-ITOH&KAZE | |||
| 25 | 6 | Exit Repair | 2'15.313 | 0.993 | 2/4 | CBR1000RR | Team OSG & Motorsports | |||
| 26 | 16 | Yoshimasa Kawase | 2'15.832 | 0.519 | 4/4 | GSX-R1000K7 | WINs SUZUKI R.T | |||
| 27 | 30 | Yuki Hatano | 2'16.094 | 0.262 | 7/7 | GSX-R1000K7 | Moto Map SUPPLY | |||
| 28 | 37 | Shinya Harada | 2'16.662 | 0.568 | 7/7 | CBR1000RR | TEAM D Kanto Funabashi R& Toriko | |||
| 29 | 35 | Atsuyuki Kobayashi | 2'21.083 | 4.421 | 5/7 | CBR1000RR | Honda Blue Helmet MSC | |||
| 30 | 704 | Tomoya Nakamura | 2'32.724 | 11.641 | 2/2 | CBR1000RR | Meiwa Racing | |||
| 31 | 70 | Hideyoshi Yoshii | Did not participate | GSX-R1000 | Fukushima Ophthalmology Clinic teamJUNBO | |||||
| Above, determined in Round 1 session. | ||||||||||