Valentino Rossi concedes Ducati is still fundamentally lacking pace compared to its rivals.
Several upgrades, including a new chassis and swing-arm, had kindled hope of genuine progress, particularly when Valentino Rossi finished second at Misano.
The Italian insisted that seventh was the maximum he could have achieved at Motegi however, with work still needed in several problem areas.
"Today I rode at the maximum for the whole race, I tried to catch Bradl, and I got closer near the end," Rossi said.
"I think we did the best that we could over the whole weekend. We worked well on the bike, and I had a good setting for the race today.
"Unfortunately, this is our potential at the moment, and our pace still isn't at the same level as the others, especially in the early laps.
"I think we've found consistency since we've had the new frame and swing-arm, but there's still work to do.
"We still lose a lot on acceleration, where we're not able to put all the horsepower to the ground because the tyre spins too much, especially exiting the slower corners."
Team-mate Nicky Hayden, who narrowly beat Yamaha wild card rider Katsuyuki Nakasuga to eighth, said he too had struggled with the handling of his Ducati.
"It wasn't a great race for me," he said.
"We were a little bit behind all weekend, but then this morning we thought we had made up some ground. In the race, though, I was having troubles getting the bike stopped, especially in the early laps.
"I lacked front feeling and was running wide, and although that improved as the race went on, I also had problems with vibration from the rear and didn't have a very good pace.
"Normally our bike is really good in straight-line braking, so it's a shame Vale and I struggled here, but anyway, it's good to finish a race and have something to build on."