The Yamaha riders hope the rain showers that hit Friday practice at Le Mans do not continue into the weekend, having been frustrated by the lack of dry running today.
Valentino Rossi and Jorge Lorenzo were sixth and seventh quickest in the session, which was hit by rain just after its halfway point.
"We always seem to have bad luck with the weather here," said Rossi. "The conditions weren't easy today, it was quite cold and the track wasn't so good, and then it rained and so we couldn't use all of the session.
"It was still useful to get some laps done in the dry though, even if we couldn't learn as much as we would have liked to today. Every lap has its own small problems and during the first rain break we made some modifications to our setting and actually I was quite confident that we were on the right track.
"We hoped to get a few more laps before the end of the session once the rain stopped but unfortunately it started again and so we had no real chance to check our work. We know we're fast in the rain but I prefer it dry... the problem is that you never know with Le Mans, the weather seems to change every five minutes."
Lorenzo was also concerned about the lack of time to work on his set-up.
"It's a pity about the rain because we needed the time today, but this is the situation so we have to deal with it," he said.
"I just hope it doesn't continue. At least we had some dry track time but the situation of the track wasn't so good and I was quite slow. We need time at each circuit to learn how our bike works with the Bridgestone tyres and we didn't really have enough time today, but we will keep trying tomorrow and hopefully we can improve our pace."
Team boss Davide Brivio hoped that at least the wet running Yamaha managed today would be useful if the rain continued.
"Luckily we had 30 minutes before it rained, because we know that this is going to be a difficult weekend where the weather is concerned," he said.
"It looks like it's going to be unsettled for the next two days so we have to take what we learnt today and use it to the best of our advantage. We still need to do some work because we didn't really get the chance to check the work we did today, so we're looking forward to more time on-track tomorrow."