Ben Spies narrowly missed out on a front row start after a strong qualifying at Motegi left the Texan in fourth place on the Factory Yamaha M1.
Spies, who held provisional pole by almost half a second over the chasing pack at the mid-way point in qualifying, looked poised to hand Yamaha a one-two on the front row alongside team-mate Jorge Lorenzo until a small error thwarted his chances.
The American star lost time on a crucial fast lap as the session reached a climax and dropped to fourth position, just 0.367s adrift of Lorenzo's pole time.
Spies, whose season has largely been blighted by terrible luck, is satisfied with the result even though he feels he had the pace to nail down a place on the front row.
“It was a good session for us, we made a small mistake at the end but the pace of the bike is good,” he said.
“By the time we got to the third rear tyre the front was a little bit past the limit but we were still pushing because I thought we could get on the front row.
“On the second tyre I made a small mistake on the hot lap which is a shame because I think that lap could have been close to pole, definitely the front row anyway and maybe a Factory Yamaha one-two,” added Spies.
“Fourth is good though as we now have a starting position so I'll give it my best for a good start and get on the back of the guys and see what we can do.”