Marc Marquez okazał się najszybszym zawodnikiem podczas deszczowego drugiego treningu wolnego na torze Motegi! Drugi czas osiągnął Jorge Martin, trzeci był Jack Miller.
| POS | RIDER | NAT | TEAM | TIME/DIFF | LAP | MAX |
| 1 | Marc Marquez | SPA | Repsol Honda (RC213V) | 1’55.232s | 8/16 | 302k |
| 2 | Jorge Martin | SPA | Pramac Ducati (GP22) | +0.144s | 10/19 | 304k |
| 3 | Jack Miller | AUS | Ducati Lenovo (GP22) | +0.155s | 14/15 | 303k |
| 4 | Miguel Oliveira | POR | Red Bull KTM (RC16) | +0.196s | 16/18 | 295k |
| 5 | Johann Zarco | FRA | Pramac Ducati (GP22) | +0.398s | 9/18 | 303k |
| 6 | Franco Morbidelli | ITA | Monster Yamaha (YZR-M1) | +0.936s | 13/16 | 295k |
| 7 | Enea Bastianini | ITA | Gresini Ducati (GP21) | +0.965s | 14/16 | 299k |
| 8 | Alex Marquez | SPA | LCR Honda (RC213V) | +1.117s | 17/18 | 301k |
| 9 | Luca Marini | ITA | Mooney VR46 Ducati (GP22) | +1.316s | 15/16 | 303k |
| 10 | Fabio Quartararo | FRA | Monster Yamaha (YZR-M1) | +1.329s | 11/19 | 298k |
| 11 | Aleix Espargaro | SPA | Aprilia Racing (RS-GP) | +1.345s | 12/13 | 300k |
| 12 | Fabio Di Giannantonio | ITA | Gresini Ducati (GP21)* | +1.356s | 16/17 | 302k |
| 13 | Marco Bezzecchi | ITA | Mooney VR46 Ducati (GP21)* | +1.423s | 15/17 | 297k |
| 14 | Cal Crutchlow | GBR | WithU Yamaha RNF (YZR-M1) | +1.511s | 15/16 | 292k |
| 15 | Francesco Bagnaia | ITA | Ducati Lenovo (GP22) | +1.520s | 15/17 | 303k |
| 16 | Remy Gardner | AUS | KTM Tech3 (RC16)* | +1.619s | 12/19 | 287k |
| 17 | Takaaki Nakagami | JPN | LCR Honda (RC213V) | +1.642s | 16/18 | 294k |
| 18 | Maverick Viñales | SPA | Aprilia Racing (RS-GP) | +1.693s | 14/15 | 298k |
| 19 | Pol Espargaro | SPA | Repsol Honda (RC213V) | +1.771s | 15/15 | 289k |
| 20 | Raul Fernandez | SPA | KTM Tech3 (RC16)* | +2.060s | 16/16 | 291k |
| 21 | Darryn Binder | RSA | WithU Yamaha RNF (YZR-M1)* | +2.374s | 15/18 | 288k |
| 22 | Tetsuta Nagashima | JPN | HRC Team (RC213V) | +2.424s | 16/17 | 298k |
| 23 | Alex Rins | SPA | Suzuki Ecstar (GSX-RR) | +2.439s | 16/17 | 296k |
| 24 | Brad Binder | RSA | Red Bull KTM (RC16) | +2.595s | 14/16 | 293k |
| 25 | Takuya Tsuda | JPN | Suzuki Ecstar (GSX-RR) | +3.399s | 15/18 | 294k |
