Casey Stoner said an early brake issue cost him a chance to fight for victory at Motegi today.
The pre-race championship leader, who had been dominant in Qatar a fortnight ago, fell back from second to seventh on the opening lap and could only recover to fourth.
He felt the lack of practice mileage - due to both this year's cuts and the rain that affected Saturday's running and forced qualifying to be cancelled - had ultimately meant Ducati was unprepared for the race.
"We have had the same issues as everybody else, I suppose, in that we haven't had time to set the bike up but all in all I think we were capable of at least matching the lap times of the front guys - we just lost too much time at the start," said Stoner.
"On the warm-up lap I felt I a lot of chatter from the front brakes, they weren't smooth and I wasn't confident over the first five or six laps. I really didn't know what to do, I wasn't able to brake where I wanted to and I wasn't confident.
"Maybe I could have gone faster but I don't know how safe that would have been. Anyway, I lost a lot of positions at the beginning of the race and I spent too much time battling to get past."
Once up to fifth, Stoner was able to match the times of the Yamahas and Hondas ahead, but could not close until the final laps, when he took fourth from Andrea Dovizioso.
"When I got closer to the front it was a bit too late, unfortunately," said Stoner.
"I tried to stay as consistent as I could and when I got closer to Andrea I rode a bit harder because I saw it was possible to pass him."
He is now three points behind new championship leader Jorge Lorenzo - and pointed out that he had lost more ground last year when he had a disastrous second round at Jerez.
"We didn't lose that many points and this is a much better start to the season than last year, so we can definitely feel positive going into the next one," said the Australian.
Ducati team boss Livio Suppo agreed that Stoner had done well to minimise the damage from this race.
"It has been a strange weekend and the weather definitely hasn't helped but it has been the same for everybody," he said.
"Casey produced a great performance, showing once again his ability to ride around problems and bringing home some important points."