Casey Stoner said that his Honda was lacking rear grip and braking stability, despite the Australian topping both free practice sessions ahead of the Catalunya Grand Prix on Friday.
Stoner was over half a second than his nearest rival - Gresini Honda rider Marco Simoncelli - during the two wet/dry sessions.
But despite this, he still believe that improvements are needed ahead of Saturday's final practice and qualifying sessions.
"We would like to improve rear grip and turning on the exit, also some more stability on the brakes, but in general the bike feels good and we're confident we can go faster tomorrow," said the 2007 world champion.
"Generally, we're quite happy with the day. But unfortunately we didn't get a lot of good wet or dry track time, so a lot of time was wasted in changeable conditions and not achieving much."
Stoner also revealed that he is not riding at 100 per cent fitness, having suffered from an illness since the French Grand Prix at Le Mans last month.
"Physically I feel better than I have done in the past weeks," he added. "I've got blocked sinuses which doesn't help when I'm trying to concentrate and my ears are popping, but I'm trying to put this to one side and concentrate on the job at hand."
The Honda factory squad is down to just two bikes this weekend following the withdrawal of Dani Pedrosa through injury, but Andrea Dovizioso put his machine third quickest on the day.
He is confident of improving his machine for Saturday's running, however.
"This afternoon we started with wet conditions and then the track dried out, however, it was not wet enough so we destroyed the tyres after few laps," said the Italian.
"All in all it was a good session and we tested both soft and hard tyres in preparation for the race, in case there will be changeable weather conditions. I'm happy with the feeling with the bike."