The Repsol Honda rider explained that the fall had been the final act in a series of mishaps that left him in 14th place, on a day when he had the speed to break into the top ten.
“Some days I go into Q2 without the speed. Today I had the speed, but I don't go in!” Marquez told MotoGP.com.
“With the first tyre, I made a mistake on the last corner and then with the second tyre there was a yellow flag and the fast lap was cancelled.
“But there was a bit of a misunderstanding for me, because I didn't see that yellow flag and didn't know that my fast lap was cancelled.
“[So] I approached the last lap thinking I needed to improve on the [cancelled] '44.0. That was already a very good lap time and I lost the front in turn one.”
Had Marquez been able to keep the 1m 44.044s yelow flag lap he would have been classified seventh fastest.
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But while Marquez had the time attack speed to go straight into Q2, his race pace is a different matter.
“On race pace, we are half a second slower than the top guys. It’s a lot. But let’s see. Step by step we are trying to do our weekend,” said Marquez, who felt the leading Ducatis, KTMs and Aprilias are all currently faster than the Honda.
He also warned: “To do a step tomorrow will be difficult. I will not touch a lot of things on the bike, I'm just concentrating on my lines, on my riding style. What I changed from this morning [1m 46.0s] to this afternoon is just a little bit more risk, pushing a bit more, and I was closer to the top guys.”
Marquez was on pole in wet conditions at Motegi a year ago and, after a sunny Friday, there is a risk of rain on Saturday.
“Tomorrow it looks like there is some chance of rain. But for some reason this year in rainy conditions I didn't feel quite good. But let's see,” he said.
Team-mate Joan Mir, who unlike Marquez tried the 2024 Honda prototype on Friday, only to suffer an early fall, was the top Honda in 12th.