Dani Pedrosa may have finished second fastest on Friday at Motegi in Japan, but the Repsol Honda rider was best with problems with the RC213V in free practice.
The Spaniard, who produced his best performance of the season in the previous round at Aragon in Spain to snatch second place away from MotoGP title leader Valentino Rossi after a gripping duel, lapped in 1m 44.859s to join Jorge Lorenzo as the only riders inside the 1m 44s bracket.
However, Pedrosa was far from happy and afterwards revealed that the Honda was proving 'complicated' at the Twin Ring circuit.
“Today was a hard day because we didn't expect the bike to be this complicated to ride. We had so many problems into the turn and out of the turn,” he said.
“It's really tough to find a good compromise with the setting. But we have to keep working with the team and try to get the best setting for this layout to put the bike as high as possible.
“Anyway we struggle and we know now, but we have to try to struggle as less we can,” he added.
“Then it's more about tyre choice and race strategy, but first of all we need to find a way to put the bike in a better place.”
Pedrosa, though, is confident he has the pace to nullify the threat of the Open class riders on the extra soft tyre in Saturday's qualifying and secure safe passage straight through to Q2.
“We will see tomorrow morning how the lap times can be,” he said. “For the moment we have a good lap time and should be safe [to get directly into Q2] already, but you never can say for sure.”