Jorge Lorenzo set the pace as huge crashes involving Dani Pedrosa and Eugene Laverty marred practice at the Japanese MotoGP on Friday.
Yamaha rider Lorenzo set a time of one minute, 45.151 seconds late in second practice to top the timesheets.
But both Pedrosa and Laverty went off in worrying crashes late in the session in Motegi.
Pedrosa, ninth quickest for the day, fractured his collarbone in a highside, while Laverty was taken from the circuit on a stretcher.
The majority of riders set their quicker times in second practice.
Ducati rider Andrea Dovizioso, who topped the first session, clocked a 1:45.204 to be second fasted behind Lorenzo.
Maverick Vinales and championship leader Marc Marquez were third and fourth fastest respectively, while Cal Crutchlow, Aleix Espargaro and Valentino Rossi were all within a second of Lorenzo.