Dani Pedrosa put the 0.6sec gap between him and pacesetting Honda team-mate Casey Stoner at Losail this evening down to a tire issue.
Although Pedrosa was still second quickest behind the dominant Stoner, he was troubled by the surprise tire performance problem.
"I had a problem with the rear tire that we need to understand," he said. "It's the first issue we've had this winter with the tires, so I hope it's an exception to the rule.
"We started the practice very well, we were fast in the first exit and then we stayed with the same tire, the softer compound, for the whole session. Even if I used the same compound during the winter test without any problem for several laps, today already in the second round I felt it dropped down a lot, and in the third and last one it was even worse.
"With only 45 minutes practice, the rounds are very short and you don't have much time to make changes. Maybe the tire had a problem, maybe it dropped down a lot because with 125cc and Moto2 bikes on track the conditions were very different comparing with the test of few days ago, we don't know exactly."
Stoner had no such issues, although even he felt there was more to come from the Honda.
"We need to improve rear edge grip, this is an area we've struggled with a little so we need to improve that which will give us better turn in and exit from the corner," he said. "I'd say we're about 80 percent complete on the bike package, we have a few main areas we can improve, but this is always the case – you can always improve something, and if we do in these areas it will make us a lot more confident."
Andrea Dovizioso was back in eighth on the third works Honda. He said he had refrained from trying a qualifying-style run, and had a braking vibration.
"With four days of practice it is important to manage the tires so today we used only the hard compound to save the soft tires for tomorrow and the coming days as I expect it will only be possible to use the soft rear tire for the race," said the Italian.
"The biggest problem today was a vibration on the front when I released the brake and this limited me a lot because I was not able to push and lean as I wanted."