Valentino Rossi went quickest in the opening free practice session at Motegi, while Honda's Dani Pedrosa was injured in a crash early on.
Pedrosa fractured his left collarbone in three places when he fell on the approach to Turn 9. He is likely to be sidelined at least for this weekend, all but confirming Jorge Lorenzo as champion.
Andrea Dovizioso looked set to top the session in the absence of his Honda team-mate, but Rossi responded with a quicker lap after time had expired at the end of the session.
Dovizioso remained second, quarter of a second back, with world champion elect Lorenzo third quickest.
Aragon winner Casey Stoner was fourth for Ducati, while the Tech 3 Yamahas showed well with Ben Spies fifth and Colin Edwards seventh - sandwiching Hiroshi Aoyama's Interwetten Honda.
Hector Barbera, Loris Capirossi and Marco Simoncelli completed the top 10.
Pedrosa was far from the only rider to hit trouble during the hour, but the others escaped any injury.
Spies dropped his Yamaha running wide on the entry to Turn 3 and Nicky Hayden later fell from his Ducati at the Turn 10 hairpin, but both walked away unscathed.
Randy de Puniet, Marco Melandri and Aleix Espargaro all survived trips into the gravel without coming off.
Pos Rider Team Time Gap Laps
1. Valentino Rossi Yamaha 1m48.174s 27
2. Andrea Dovizioso Honda 1m48.387s +0.213 26
3. Jorge Lorenzo Yamaha 1m48.474s +0.300 27
4. Casey Stoner Ducati 1m48.481s +0.307 19
5. Ben Spies Tech 3 Yamaha 1m49.302s +1.128 27
6. Hiroshi Aoyama Interwetten Honda 1m49.357s +1.183 27
7. Colin Edwards Tech 3 Yamaha 1m49.377s +1.203 24
8. Hector Barbera Aspar Ducati 1m49.544s +1.370 21
9. Loris Capirossi Suzuki 1m49.568s +1.394 23
10. Marco Simoncelli Gresini Honda 1m49.581s +1.407 24
11. Marco Melandri Gresini Honda 1m49.620s +1.446 20
12. Alvaro Bautista Suzuki 1m49.644s +1.470 24
13. Nicky Hayden Ducati 1m49.882s +1.708 18
14. Randy de Puniet LCR Honda 1m49.957s +1.783 24
15. Aleix Espargaro Pramac Ducati 1m50.158s +1.984 21
16. Mika Kallio Pramac Ducati 1m51.105s +2.931 24
17. Dani Pedrosa Honda 2m00.131s +11.957 2