Valentino Rossi put his return to competitiveness in Japan down to both improvements from Yamaha and an upturn in his fitness.
The world champion had struggled all weekend at Aragon a fortnight ago, where he qualified only seventh and finished sixth.
But at Motegi Rossi has been a frontrunner from the outset, leading opening practice and taking second on the grid.
"First it's a technical difference, because we've improved the setting of our bike a lot, and the new engine from Yamaha pushes more so we are also faster on the straight," he said.
"Also here we have harder tyres compared to Aragon. For me at Aragon, the hard was too soft, so I was in a little bit of trouble."
In Spain Rossi felt the after-effects of his April shoulder injury had been a major factor in his lack of pace. He feared it would be worse still at Motegi, but has been pleasantly surprised by his physical condition.
"About the shoulder, I expected to suffer a lot more, because here there is a lot of hard braking," said Rossi. "But from yesterday afternoon I felt quite good. When I brake from straight, I don't have a lot of pain, so I can push."
Today's result is the first time Rossi has qualified on the front row since returning to the fray following his lay-off with a broken leg in early summer.
"I'm very happy to be back on the front row because it's been since Le Mans - before the crash at Mugello - that I could not be here," said the Italian.
"It will be very important for the race tomorrow. We hope to have good weather and we will see what happens."