Casey Stoner said he was “disappointed” with fifth place at Motegi on his return from injury.
The reigning MotoGP world champion, who started from seventh on the grid, felt he had the pace to match his Repsol Honda team-mate Dani Pedrosa and Yamaha's Jorge Lorenzo.
However, Stoner – who suffered ankle fractures and ligament damage following a qualifying spill at Indianapolis – struggled on the RCV as his body began to “ache” during the race.
“I'm a little disappointed to be honest. We slowly improved over the weekend and got the bike to a point we were pretty happy with in warm up,” said Stoner.
“At the start of the race I felt had the pace to stay with Dani and Jorge and the bike was feeling pretty good.
“Then as the race progressed my body started to suffer and ache in ways I didn't expect.
“We had the pace to run a lot higher and be on the podium but unfortunately I couldn't manage it physically today,” he added.
“A big thanks to my team, they gave me a fantastic bike today but I couldn't do anymore in my condition.”