ARTA duo Nirei Fukuzumi and Hiroki Otsu came to Motegi 16 points down on the championship-leading TOM'S Toyota of Sho Tsuboi and Ritomo Miyata, needing a win to have any chance of winning the title.
But any such hopes were dealt a hefty blow in the first segment of qualifying on Saturday, as Otsu ended up ninth-fastest, missing out on a spot in Q2 by a scant five thousandths of a second.
By contrast, the #3 NDDP Nissan Z of Katsumasa Chiyo and Mitsunori Takaboshi took a dominant pole, while Tsuboi and Miyata were a strong third in their Toyota GR Supra.
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The #16 ARTA had been considered a strong contender given Fukuzumi's record of two poles from the last three races, but Otsu was left to rue the Mugen-run squad's decision to go with a different Bridgestone tyre to the other Honda squads.
"It was a tough qualifying," Otsu told Motorsport.com. "I don’t feel I made any mistakes, and I just thought if I could put everything together it would be ok, but our opponents improved more than we expected.
"We went a different way on tyre choice and I think honestly it didn't work out. Everyone else besides us was on the same tyre and I don’t think we had the peak grip as the others.
"At the least I would have liked to have gotten out of Q1, so it’s frustrating I couldn’t do that, so I want to say sorry to Nirei and the team."
Otsu admitted however that even had he been able to clear Q1, the pace of the NDDP Nissan, in which Chiyo went nearly four tenths clear of the field, was not possible to match.
"There’s no way we could have been on pole with our current potential," he added. "The #3 Nissan was on another level, I was quite surprised.
"I think it might have been possible to be around third, fourth or fifth, but that honestly feels like our current level of performance."
Even if Fukuzumi and Otsu win from ninth on the grid, they would still need both the NDDP Nissan and TOM'S Toyota crews to hit trouble to win the title in what will be the NSX-GT's last race before it is replaced by the Civic Type R-GT.
Either a top-six finish for Tsuboi and Miyata or a top-three for Chiyo and Takaboshi would be enough to deny the ARTA Honda pair.
"Even though there's almost no chance, as long as there’s a small chance, we have to try our best," said Otsu when asked how he felt about the title situation.
"Although we’ve often started near the front lately, this time we have to fight our way forwards from the mid-pack, but if we can bring out the car’s potential I think we can still get involved in the fight for the lead positions.
"I think aiming solely for the title from our position would be crazy, but it would be good to try and get at least one place higher in the rankings. If we win, the championship could still come as a bonus, so I want to do my best without giving up."