Pedrosa's fastest lap of 1 minute, 46.790 seconds around the Twin Ring Motegi circuit was five hundredths of a second better than his Repsol Honda teammate Casey Stoner of Australia. Spain's Andrea Dovizioso was third fastest.
Stoner, who won here last year, has a 44-point lead over 2010 world champion Jorge Lorenzo with four races to go. Lorenzo was fifth in Friday's practice.
Thomas Luthi of Switzerland had a fastest lap of 1:53.002 in the Moto2 category while Spain's Maverick Vinales was fastest in the 125cc practice with a time of 1:59.273.
Sunday's race was originally scheduled for April, but was postponed after the March 11 earthquake and tsunami that triggered a radiation leakage from a damaged nuclear power plant.
Several riders, including nine-time world champion Valentino Rossi, considered skipping the Japan Grand Prix because of radiation concerns after the earthquake and tsunami.
Twin Ring Motegi is 149-kilometers (93 miles) from the Fukushima-Dai-ichi nuclear plant, which leaked radiation after being severely damaged by the earthquake and tsunami. - http://timesofindia.indiatimes.com