Jorge Lorenzo edged out his MotoGP title rival Dani Pedrosa by 0.141 seconds in a close battle in opening practice at Motegi.
Lorenzo initially put his Yamaha 0.7s clear of the field, before Pedrosa's Honda got within 0.014s of the benchmark.
A late improvement then stretched Lorenzo's advantage to nearly two tenths of a second, as the championship leader lapping in 1m46.558s.
Pedrosa also went quicker, but could only manage a 1m46.699s so had to settle for second.
Casey Stoner marked his return to the second Honda after his injury absence with fourth place. The reigning champion was 0.6s down on team-mate Pedrosa as he assessed his fitness.
Tech 3 Yamaha's Andrea Dovizioso split the two Hondas in third. Fellow Yamaha men Ben Spies and Cal Crutchlow completed the top six.
The works Ducatis were back in seventh and 10th with Nicky Hayden and Valentino Rossi.