Valentino Rossi had to settle for the third row during qualifying at Motegi after failing to hit his target of a top six position.
Rossi had set the fifth fastest time on his Factory Ducati Desmosedici during opening practice on Friday and had hoped to secure a similar result in qualifying.
The Italian MotoGP star ended up ninth quickest but was content with his time, which represents an improvement of 0.5s over his best lap at the Japanese circuit in 2011.
“The position, ninth place, certainly isn't the greatest, as I had hoped to start from the second row,” said Rossi, who was one second adrift of Jorge Lorenzo's pole time.
“Still, I think that we worked well. We improved in every session, and again in qualifying today we made good progress.
“1:45.9 is a nice time, half a second faster than last year, even though it wasn't enough to be further forward,” he added.
“Anyway, we managed to lap at a decent pace and more consistently, and that's positive.
“Tomorrow we'll see if it will be enough and if we'll be able to move up some positions.
“We'll also have to decide tomorrow which tyre to use, depending on what the temperature is.”