Qualifying #1  Weather:Fine | Course:Dry | Air Temp. 19° | Track Temp. 30°

The first official qualifying session began at 10:20. The track surface was dry and the temperature at the start of the session was 19 degrees C., with a track surface temperature of 30 degrees.

The first 20 minutes were for the GT300 class. The first car to post a top time was the No. 88 AKTIO MURCIE RG-1 (Marco Apicella) at 1 min. 42.515 sec. The next fastest time after that came from the No.43 ARTA Garaiya (Morio Niita) and the third fastest was by the No. 26 YUNKER-POWER TAISAN PORSCHE (Shinichi Yamaji) . They were followed by the No. 2 Priv_e KENZO Asset Shiden (Hiroki Katoh) in 4th and the No.33 HANKOOK NSC PORSCHE (Mitsuhiro Kinoshita) in 5th place. The Porsche machines clearly showed their speed advantage on the Fuji Speedway's long straights. After them came the No. 46 houzan DUNLOP Z (Kota Sasaki) , the No. 101 TOY STORY Racing apr MR-S (Kazuya Oshima) , the No. 62 WILLCOM ADVAN VEMAC408R (Shinsuke Shibahara) , the No. 7 RE AMEMIYA RX-7 (Hiroyuki Iiri) and the No. 31 apr MR-S (Kyosuke Mineo) to fill out the top ten qualifiers for the Super Lap.

The next 20 minutes were for the GT500 class. It wasn't until the last three minutes of the session that the teams began their serious timed runs. The first to take the lead with a time in the 1 min. 34 sec. range was the No. 38 ZENT CERUMO SC430 (Yuji Tachikawa) . Immediately after that, the No. 25 ECLIPSE ADVAN SC430 (Takeshi Tsuchiya) turned in a better time. Then the No. 18 TAKATA DOME NSX (Takashi Kogure) ran a time under 1 min. 34 sec. and bettered that on the next lap with a 1 min. 33.697 sec. lap to consolidate its lead. No. 8 ARTA NSX (Daisuke Ito) followed with a 1 min. 34.261 sec. lap. No. 38 attempted a lap after that only to spin out on the last corner. In order to avoid colliding with No. 38 as it spun out, the No. 1 Houzan TOM'S SC430 (Andre Lotterer) lost considerable time. Despite this, No. 1 was still able to place 3rd, but No. 38 ended up in 9th place.

In the final 20-minute mixed session there were no cars that were able to improve their position. As a result, the Super Lap qualifiers for the GT500 class were the No. 18 TAKATA DOME NSX, the No. 8 ARTA NSX, the No. 1 Houzan TOM'S SC430, the No. 17 REAL NSX (Toshihiro Kanaishi) , the No. 25 ECLIPSE ADVAN SC430, the No. 39 DENSO SARD SC430 (Andre Couto) , the No. 32 EPSON NSX (Loic DUVAL) , the No. 100 RAYBRIG NSX (Dominik Schwager) , the No. 38 ZENT CERUMO SC430 and the No. 12 CALSONIC IMPUL Z (Benoit Treluyer) .

Qualifying #2/Super Lap  Weather:Fine | Course:Dry | Air Temp. 21° | Track Temp. 30°

The second qualifying session for all the contestants began at 15:10. The GT300 class ran the first 15 minutes, followed by the GT500 class in the next 15 minutes. At the start of the session the air temperature had risen slightly from the morning session to 21 degrees C. and the track surface temp. to 30 degrees. After a crash in the previous day's practice, the No. 111 KUMHO GREEN-TEC BOXSTER-GT was finally able to make an appearance in this session. Replacing driver Takeshi Namekawa, who suffered a head injury from that crash, Takaya Tsubobayashi took the wheel. Together with the team's first driver, Yasushi Kikuchi, Tsubobayashi was able to get a qualifying time and proceed to the final. In contrast, the No. 67 triple a GALLARDO RG-3 was unable to get a qualifying time and will have to await a decision following its performance in the free run in the morning of race day.

The Super Laps began with the GT300 class. The first runner, the No. 31 apr MR-S (Kyosuke Mineo) improved on its morning time by a big margin, indicating that a hot race for the pole position would follow. The next in order, the No. 7 RE AMEMIYA RX-7 (Hiroyuki Iiri) , was unable to make its time trial due to sensor malfunction in the engine. The third runner, the No. 62 WILLCOM ADVAN VEMAC408R (Shinsuke Shibahara) turned in a 1 min. 42.185 sec. time, more than 0.3 seconds faster than the morning session's fastest qualifying time. This became the initial target time for the remaining machines. Just after that, the No. 101 TOY STORY Racing apr MR-S (Kazuya Oshima) and the sixth runner, the No. 33 HANKOOK NSC PORSCHE (Mitsuhiro Kinoshita) ran exactly the same time of 1 min. 42.309 sec. to stand even behind No. 62. This meant that No. 33, one of the morning's leaders was now behind No. 101 in the starting order. After that, the No. 26 YUNKER-POWER TAISAN PORSCHE and the No. 43 ARTA Garaiya were unable post times faster than No.62 and the following pair. Thus, seemed for a moment that Shinsuke Shibahara was about to set a new record for most pole positions by a driver. But the final runner, the No. 88 AKTIO MURCIE RG-1 (Marco Apicella) , ran very fast in the last sector of the course after trailing No. 62's time slightly through the first two sectors and managed to cross the finish line at 1 min. 42.112 sec. to claim the class pole position. This was the first PP for Apicella since the 2006 round five at Sugo.

Next began the GT500 class Super Lap. The No. 12 CALSONIC IMPUL Z (Benoit Treluyer) was the first to take to the course. Treluyer was pushing to the very limits of control with the team's new machine that still had some set-up work left to be done. He managed to shave more than 0.5 seconds off his morning time with a 1 min. 33.949 sec. lap. The next five machines to run were unable to better this time and it wasn't until the seventh runner, the No. 17 REAL NSX (Toshihiro Kanaishi) , that a faster time appeared. However, the next runner, the No. 1 Houzan TOM'S SC430 (Andre Lotterer) , ran an even faster time to take way that short-lived lead. As for the morning's second fastest qualifier, the No. 8 ARTA NSX (Daisuke Ito) , it was unable to overcome the disadvantage of its 65kg of weight handicap and fell short of No. 1's leading time. The final attacker was the No. 18 TAKATA DOME NSX (Takashi Kogure) . Kogure, who had run more than 0.4 seconds faster than the next fastest qualifier in the morning session, ran a time of 1 min. 33.066 sec., which beat the course record set by Yuji Tachikawa (ZENT CERUMO) in 2005 by 0.04 sec. For No. 18, this was the second pole position in two consecutive rounds, following Ryo Michigami's PP in the previous round at Okayama. This gave the NSX teams their third consecutive pole position since the season opener. For the SC430 teams, the 2nd place of No.1 Houzan TOM'S SC430 was the top performance. For the Fairlady Z teams, the 5th by No. 12 CALSONIC IMPUL Z was the best performance.

In the post-qualifying inspection, it was found that No. 25 in the GT500 class and No. 101, No. 62, and No. 31 in the GT300 class failed to meet the minimum ground clearance regulation, and the Super Lap time of the No. 46 Houzan DUNLOP Z was deemed invalid because the machine had run off the designated course during its run.