The Honda rider is just 28 points behind championship points leader Yamaha ace Jorge Lorenzo with three rounds remaining this season, including in Sepang.
Title-hopeful Pedrosa, who is battling for his first ever MotoGP crown, clocked 2min 01.621sec in the first session on a dry surface.
Pedrosa’s Australian teammate and reigning world champion Casey Stoner, who is recovering from an ankle injury, clocked the second best time of 2:01.773.
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