The recurrent wrist problem hampered Stoner for much of the second half of 2008, but he waited until the off-season for the necessary operation and hoped he would be fully fit by the time preparations for 2009 began.
However while Stoner was second-fastest in Malaysia today, he was still in discomfort from the operation.
"This morning was really difficult, I really didn't feel comfortable on the bike," said Stoner.
"My wrist is still in a lot of pain and I honestly hoped it would be in better shape than this after three months since the operation.
"Even though the lap times were good from the start the wrist was still giving me a lot of problems - it is weak and painful under braking, especially in the first left-hand turn.
"I can't do more than four or five laps at a time and there's nothing I can do about that at the moment, other than hope that it improves over time. Sepang is a physically demanding circuit and probably not the best place to be riding for the first time after three months out.
"I preferred not to ride too much and tire myself out and hopefully it will already be a bit better tomorrow. Freddy, our physiotherapist, has a bit of work to do tonight."
Stoner was more positive about the 2009 Ducati, which features a radical carbon fibre frame.
"The chassis is completely different and we'll have to work on improving the set-up but we have a good starting point and we can use the GP8 as a reference," he said.
"The power delivery has improved and now we have more torque, which helps on the exit of the slower corners."
Ducati's second rider Nicky Hayden continued to struggle to get up to speed on the bike, and was only 11th quickest - two seconds adrift of Stoner. But he said the team were getting closer to a solution to his problems.
"We started out with the same set-up as Jerez, because after two months without riding it was better to go with something we knew," Hayden said.
"We haven't made massive changes over the course of the day, mainly because before we do that I need to pick up my own pace. The bike feels good on the brakes and it is stable and precise in the fast corners.
"I'm struggling a bit on corner exit though because it still tends to pump quite a lot and I'm not used to that yet. We're working to reduce it and we've got a couple of ideas that we'll check out over the next two days."
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