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Pedrosa, 63 points behind compatriot Jorge Lorenzo in the championship standings, clocked 1min 50.506sec in the morning session before rain slowed down proceedings in the afternoon.
"In general this has been a good first day of practice for us at a brand new circuit for MotoGP," said the 24-year-old Pedrosa.
"This morning we started well and got into a rhythm quickly, which was important because it makes a big difference going from the one hour practice sessions we're familiar with to 45 minutes.
"It's necessary to stay out on track for longer runs and not spend too long in the garage, and this morning we did a good job to maximise our time."
Pedrosa penned a new two-year deal to keep him at Honda until 2012 and he believes the partnership can only go from strength to strength.
"I’m very happy to be continuing with Honda for another two years. It's been a long relationship and also a successful one, and I hope we can be even more successful over the next two years," he said.
Ducati rider Nicky Hayden of the United States was second fastest, 0.411sec off the pace with Lorenzo on a Honda in third, 0.422sec off the lead.
Australian teammate Casey Stoner, Honda's Marco Simoncelli and reigning world champion Valentino Rossi, on a Yamaha, made up the top six.
"This morning we were second in the dry and then in the afternoon we were third in the wet so it's been a good day," said Hayden, who has yet to make the podium this season.
