The Yamaha rider has traditionally struggled in wet conditions on the M1, but was strong in March in the rain-hit Indonesian GP when he finished second – and was inside the top 10 in FP2 on Saturday morning at Motegi.
But Quartararo could do no better than ninth in qualifying, missing pole by 1.1 seconds.
The Frenchman was unable to make any improvements on his initial 1m56.326s flying lap and doesn’t understand how that is possible when his rivals can manage it.
“Not happy because I expected much better,” Quartararo said.
“I still don’t understand how it’s possible to go into Q2, first lap do a 1m56.7s and then all the qualifying the same – no improvement.
“I have a feeling, then when we check the data and it’s not the same.
“So, I’m a little bit lost in this track on the wet.
“The feeling is good, but how to make the lap time… we were one second from the pole.
“It’s a lot, but compared to what it used to be it’s not so bad. But it’s difficult to understand.”
Quartararo starts between his main championship rivals Francesco Bagnaia in 12th and Aleix Espargaro in sixth for Sunday’s Japanese GP – which is expected to be run in dry conditions.
He is wary of the fact his options to overtake on the Yamaha will be limited relative to the Ducati and the Aprilia.
“The only problem is the facilities they have compared to us to overtake,” he said when asked if he would only focus on where his rivals are in the race.
“This is the problem. So, I’m more worried about that and where I can overtake, because every braking [zone] is after a straight.
“So, this will be my main problem in the race. But I feel ready and I feel we can do something.
“At the moment, only Turn 7 [is where I can overtake] and that is not really a place to overtake. But if I want to overtake, it’s the only place I can.”
Espargaro “wants to win” but must “use your brain”
Aleix Espargaro struggled for much of the wet morning session at Motegi on Saturday, but managed to put his Aprilia onto the second row in sixth – just 0.557s away from Marc Marquez’s pole time.
The Spaniard – who is 17 points off the championship lead currently – admits it’s hard to know how his race will go given how much work Aprilia needed to do in the dry FP1 on Friday to make his bike competitive.
However, while he knows he has to be aware of his main title rivals, he believes he can fight for the race win.
Asked what he could expect from the race, Espargaro said: “It’s difficult to tell you.
“I don’t know what to expect, sincerely. Yesterday the bike was very for from being competitive.
“From 2019 to here, the Aprilia is another world. I changed the gears in five corners, we changed the gearbox [to find] more than 20km/h, we changed the balance, the electronics.
“So even like that on Friday we were very fast.
“So, I think tomorrow can be a good day for us. You have to use your brain, but I want to win tomorrow.
“I think I have a good opportunity. I’m fast, the bike works quite good, the grid is a little bit strange. But obviously you have to be aware of them and analyse the situation.
