| Pos | No. | Name | Time | Delay | Gap | Lap | Type | Team | ||
| 1 | 41 | Yuichi Ui | 1'56.768 | 148.03Km/h | 7/7 | TZ250 | PRO-TEC&Spruce | |||
| 2 | 4 | Takashi Takumi | 1'58.457 | 1.689 | 1.689 | 5/8 | RBB250 | Burning Blood RT | ||
| 3 | 56 | Yamazaki District | 1'58.501 | 1.733 | 0.044 | 8/8 | TZ250 | HITMAN RC Motegi Yamaha | ||
| 4 | 16 | Daikou Sakurai | 1'59.577 | 2.809 | 1.076 | 8/8 | RS250R | KEIHINKoharaR.T. | ||
| 5 | 8 | Takashi Akita | 1'59.649 | 2.881 | 0.072 | 8/8 | TZ250 | HenkelTDRYAMAHA | ||
| 6 | 14 | Rei Oikawa | 2'00.143 | 3.375 | 0.494 | 6/6 | TZ250 | Pentagram & �Gama Shou & M-Ra | ||
| 7 | 15 | Hiroshi Toyota | 2'00.145 | 3.377 | 0.002 | 6/8 | TZ250 | D:REX | ||
| 8 | 48 | Tomisawa Shoya | 2'00.196 | 3.428 | 0.051 | 3/7 | RS250 | TeamProjectμFRS | ||
| 9 | 5 | Masato Oikawa | 2'00.206 | 3.438 | 0.010 | 6/6 | TZ250 | Will Access & Plus View | ||
| 10 | 6 | Akitsuya Morimori | 2'00.335 | 3.567 | 0.129 | 7/8 | TZ250 | Team Moto Space | ||
| 11 | 19 | Yuki Ito | 2'00.873 | 4.105 | 0.538 | 7/7 | TZ250 | DOG FIGHT RACING | ||
| 12 | 45 | Doni Tata Pradita | 2'01.749 | 4.981 | 0.876 | 7/7 | TZ250 5KE4 | Yamaha Indonesia RT | ||
| 13 | 31 | Kazuki Watanabe | 2'02.095 | 5.327 | 0.346 | 8/8 | TZ250 | TeamDankeRacing | ||
| 14 | 34 | Riko Oguchi | 2'02.622 | 5.854 | 0.527 | 6/6 | TZ250 | ALLMAN&OW Oguchi Dental Clinic | ||
| 15 | 25 | Fukuyama Kyota | 2'02.760 | 5.992 | 0.138 | 7/7 | TZ250 | TeamDankeRacing | ||
| 16 | 65 | Akira Nibe | 2'02.783 | 6.015 | 0.023 | 6/7 | TZ250 | SP-X& Kotobuki Racing | ||
| 17 | 26 | Shibahara Makoto | 2'02.916 | 6.148 | 0.133 | 7/8 | TZ250 | TeamDankeRacing | ||
| 18 | 62 | Nakamoto-gun | 2'03.017 | 6.249 | 0.101 | 5/7 | TZ250 | RT・OUTRUN | ||
| 19 | 93 | Takumi Endo | 2'03.641 | 6.873 | 0.624 | 6/7 | TZ250 | PRO-TEC & Niigata Industrial College | ||
| 20 | 47 | Koguchi Wataru | 2'04.944 | 8.176 | 1.303 | 5/6 | TZ250 | ALLMAN&OWRACING | ||
| 21 | 28 | Hikaru Oshiro | 2'05.933 | 9.165 | 0.989 | 7/7 | RS250R | Oshiro R・Kaneda Industries | ||
| 22 | 7 | Hiroki Hamamoto | 2'06.463 | 9.695 | 0.530 | 5/5 | TZ250 | TEC2&Feel. Kyushu Kyoritsu University | ||
| 23 | 72 | Kimura Asahi Atsushi | 2'06.481 | 9.713 | 0.018 | 7/7 | TZ250 | PRO-TEC Nihon University Faculty of Engineering Mechanical Research | ||
| 24 | 36 | Hiroki Iizuka | 2'12.763 | 15.995 | 6.282 | 4/4 | TZ250 | Garage Kokusei & Iizuka Automobile Trading | ||
| 25 | 27 | Kazuki Saito | 2'18.027 | 21.259 | 5.264 | 6/6 | RS250R | Power Pipe MRF |