Viñales stuck his M1 in P1 early on in FP1 and then put his energy towards working on his bike‘s set-up to make it match the Twin Ring Motegi track‘s stop-start nature. He gradually improved his time, achieving provisional first place once more 25 minutes into the session, although it didn't last long. But when a mini time attack started in the final five minutes, the number-12 rider was ready for the fight and reclaimed the top spot. Quartararo put in a late challenge, but the Factory team rider retaliated with a 1‘45.572s, ending the session in first place with a 0.258s advantage over second, for an early Yamaha 1-2-3.
The Spaniard also booked steady progress in the afternoon practice. He spent a large part of the session near the top of the provisional rankings, until the latter stages, when he put in a soft rear tyre for his final outing and dropped a fast time to top the session again for a short while. His best lap of 1'45.085s was 0.321s from the top and left him in second place in the FP2 and the combined free practice standings.
Rossi got off to a positive start at Yamaha‘s home GP. He briefly moved up to third place and started to work on race pace, like he announced he would before coming to the Japanese GP venue. He was eager to work on riding with used tyres, especially as the nine-time World Champion knows like no other how wearing the Motegi track can be. The Italian was so fixed on this task that he did not come in for a fresh set of tyres to put in a hot lap at the end of the morning session, like the majority of the rider field. He took 12th position, 0.848s behind his team-mate.
Rossi continued to test various setting options as well as some tyre specs in FP2, leaving it until the final seconds to put in a hot lap because of an issue with his first bike. Though the second bike had a different set-up, the nine-time World Champion quickly adjusted. The window of opportunity was extremely narrow when he started his fourth and final run just a couple of minutes before the end of the session, but the Doctor remained calm and collected. He crossed the start-finish line for his flying lap with 10s to spare, and gave it his all for a 1'45.466s, to take fifth in the FP2 and combined session results, 0.702s removed from first.