Defending champion Bagnaia leads Martin in first Japan MotoGP practice
Italy's Bagnaia clocked a fastest lap of 1min 45.209sec on his Ducati, with more than half of the 45-minute session wiped out by rain at Motegi.
Spaniard Martin, who leads Bagnaia by 21 points in the championship standings with five races remaining, trailed his rival by 0.109.
Pramac rider Martin is looking to win his first MotoGP championship after finishing second behind Bagnaia last year.
Italian Fabio Giannantonio clocked the third-best practice time, 0.380 behind Bagnaia, while Spain's six-time world champion Marc Marquez was fourth, 0.572 off the leading pace.
Italy's Enea Bastianini, who is third in the overall standings and trails Martin by 75 points, had the 10th-fastest practice time, 0.759 behind Bagnaia.
The riders went out for around 15 minutes under cloudy skies before rain halted the session.
The action later resumed for around five minutes before rain again forced them back to the garage.
The second practice session, from which the top 10 riders go straight into Saturday's second round of qualifying, gets underway at 15:00 (08:00 CET).
Qualifying shapes the grid for both the sprint race on Saturday and the main event GP on Sunday afternoon, with a maximum of 37 points available.