Ducati team-mates Casey Stoner and Nicky Hayden both ended Friday practice at Sepang in a frustrated mood, having been unable to match the pacesetters.
Stoner was briefly quickest early on before having a minor crash, and could not improve on fourth when he resumed running.
Hayden fared far worse - struggling to 15th place, 0.8 seconds slower than his team-mate.
Stoner said a variety of small issues had hampered his session.
"I'm not really happy with the way things went today," he said. "We had a small crash at the beginning of the session so had to switch bikes and do a lot of work to get it feeling better.
"Every time I went out there was some small problem and we seemed to take a while to find a reasonable setting. By the end I had established a good feeling and I wanted to make a better lap time on the second lap of my final run but I ran wide in Turn 1 and that was that.
"We'll take this data and try to improve the bike for tomorrow. We seem to be struggling most of all with the rear, just like at Motegi, but once we solve that I'm sure we'll see major improvements with the rest of the bike."
Whereas Stoner was able to recover from a poor practice result and take victory in Japan, Hayden was off the pace all weekend at Motegi - and was concerned that his Malaysian Grand Prix weekend was starting in the same fashion.
"We have picked up where we left off in Japan, which is not a good thing," said the American.
"We struggled a lot, right from the beginning, over the bumps mainly. I have a lot of front chatter, we got rear chatter too, and I cannot carry any good corner speed.
"We're 1.2 seconds off the top, which may not seem that much but the reality is that it is a lot when the field is as tight as it is right now. That kind of gap is pretty much going to send you to the back.
"We definitely need to do something for tomorrow because today was not good."