Nicky Hayden was unable to find his groove as he struggled to 10th position during final qualifying at Motegi.
The Ducati rider, who is nursing an injured right hand following his terrifying spill at Motorland Aragon last time out, will start from the fourth row of the grid for the Japanese MotoGP at the Twin Ring circuit, almost one-and-a-half seconds behind pole man Jorge Lorenzo.
A downbeat Hayden said: “Today didn't really go any easier than yesterday. I had some problems at the start of qualifying and couldn't get a good rhythm, but once I started putting the soft tyres in, the grip improved and the bike felt better and better.
“Then at the end, I had a lot of front chatter that was holding me back, including on my best lap, and there were a lot of waving yellow flags on my last run that didn't help.
“Unfortunately, I didn't really get in a good lap, and I didn't have a good rhythm either,” he added.
“Still, the team is working hard and hopefully tomorrow we can improve and try to do a decent race.”