The Finn, who failed to finish the Formula One season-opener in Australia last week due to engine problems, was left stranded in the morning session as his Ferrari spluttered on vapours and then stopped out on the track.
He had no option but to abandon the car and watch as it was unceremoniously hoisted off by a crane.
Ferrari blamed confusion in the pit lane.
“This morning we got our lines of communication mixed up between the garage and the pit wall, which left Kimi stuck on the track without any fuel,” said Ferrari’s head of track activities Luca Baldisserri.
“But in the afternoon we were able to get more done, without any technical problems whatsoever.”
Raikkonen overcame the early setback to record the second fastest time in the morning behind team mate Felipe Massa and was then third quickest in the afternoon practice.
McLaren’s Lewis Hamilton posted the fastest time of the day late in the second session.
“This morning I lost time because of a communication problem within the team but we made up for it in the second session,” said the 28-year-old.
“The car seems to be going well and I am pleased with the work we have done. It’s always difficult to say where we are compared to our rivals, but I think we can face the rest of the weekend with confidence.”
Ferrari are hoping for a positive performance in Malaysia after a nightmare start to the season in Australia. Neither Raikkonen nor Massa reached the finish line as the Italian team suffered their worst start to a season since 1992.