Honda rider Dani Pedrosa narrowly missed breaking the Sepang lap record but still led the standings after Friday's two practice sessions ahead of the Malaysian Grand Prix.
The Spaniard recorded a time of two minutes and 00.554 seconds - two tenths slower than Jorge Lorenzo's best time.
Championship leader Marc Marquez was second quickest, half a second behind his team-mate and compatriot.
Britain's Cal Crutchlow was third, ahead of Italian Valentino Rossi.
Reigning champion Lorenzo, who trails Marquez by 39 points in the standings with four rounds of the season remaining, was only sixth fastest, behind Spain's Lorenzo.
Britain's other rider Bradley Smith was 10th.
Marquez was given a penalty point but escaped a potential grid penalty for this weekend after a clash with Pedrosa in last month's Aragon Grand Prix.
Despite topping both practice sessions, last year's Malaysian Grand Prix winner Pedrosa said he was still feeling the effects of what happened in Spain.
"I expected to have less pain actually. But I was fast already from the beginning," he said. "If I can get a good painkiller for the race, maybe it's okay."
Lorenzo, who has admitted retaining the championship will be "almost impossible", said his Yamaha lagged behind the Hondas.
"We cannot control the performance of the other riders - we can just improve ourselves," said the Spaniard, who posted the fastest-ever lap of Sepang last year of 2:00.334.
"I have to be confident. It's the only way. If you don't feel confident or you are unhappy, it's the start of the finish."
1. Dani Pedrosa (Esp/Honda) 2min 00.554sec,
2. Marc Marquez (Esp/Honda) at 0.533,
3. Cal Crutchlow (Gbr/Yamaha) at 0.869,
4. Valentino Rossi (Ita/Yamaha) at 0.984,
5. Jorge Lorenzo (Esp/Yamaha) at 1.069
6. Alvaro Bautista (Esp/Honda) at 1.105
7. Stefan Bradl (Ger/Honda LCR) at 1.173
8. Nicky Hayden (USA/Ducati) at 1.819
9. Andrea Dovizioso (Ita/Ducati) at 1.933
10. Bradley Smith (Gbr/Yamaha) 1.997