1.
Casey Stoner AUS Ducati Marlboro Team (B)
2min 4.542 secs
2.
Dani Pedrosa SPA Repsol Honda Team (M)
2min 5.114 secs
3.
Nicky Hayden USA Repsol Honda Team (M)
2min 5.740 secs
4.
John Hopkins USA Rizla Suzuki MotoGP (B)
2min 5.846 secs
5.
Randy de Puniet FRA Kawasaki Racing Team (B)
2min 6.270 secs
6.
Alex Barros BRA Pramac d'Antin (B)
2min 6.519 secs
7.
Valentino Rossi ITA Fiat Yamaha Team (M)
2min 6.613 secs
8.
Loris Capirossi ITA Ducati Marlboro Team (B)
2min 6.631 secs
9.
Anthony West AUS Kawasaki Racing Team (B)
2min 6.721 secs
10.
Marco Melandri ITA Honda Gresini (B)
2min 6.872 secs
11.
Chris Vermeulen AUS Rizla Suzuki MotoGP (B)
2min 6.898 secs
12.
Nobuatsu Aoki JPN Rizla Suzuki MotoGP (B)
2min 6.952 secs
13.
Toni Elias SPA Honda Gresini (B)
2min 6.995 secs
14.
Carlos Checa SPA Honda LCR (M)
2min 7.272 secs
15.
Colin Edwards USA Fiat Yamaha Team (M)
2min 7.695 secs
16.
Shinya Nakano JPN Konica Minolta Honda (M)
2min 7.775 secs
17.
Kurtis Roberts USA Team Roberts (M)
2min 9.324 secs
18.
Makoto Tamada JPN Dunlop Yamaha Tech 3 (D)
2min 9.469 secs
19.
Chaz Davies GBR Pramac d'Antin (B)
2min 9.892 secs
20.
Sylvain Guintoli FRA Dunlop Yamaha Tech 3 (D)
2min 10.244 secs
2006 Malaysian Grand Prix:
Pole position: Valentino Rossi ITA Camel Yamaha (M)
2min 0.605secs (in free practice, qualifying cancelled)
Fastest race lap: Loris Capirossi ITA Ducati Marlboro (B)
2min 2.127secs
