Valentino Rossi said his first lap crash cost him the chance of fighting for the podium at Motegi, particularly with the race claiming such a high number of casualties.
Rossi arrived in Japan having made further changes to his Ducati, and was rewarded with a promising display in qualifying as he sealed seventh, having been in contention for the second row for much of the session.
He was then fourth fastest in the warm-up session, only to crash on the second turn of the opening lap of the race after making contact with Yamaha's Jorge Lorenzo.
"It's really a shame to be out of the race after two corners, especially after the progress that we made this weekend, and with the knowledge that we'd worked on the bike well," Rossi reflected.
"I was fourth in the morning warm-up, and when you also consider the troubles that Stoner, Simoncelli and Dovizioso had, we could have fought for the podium, which would have been really nice for us.
"We were a little unlucky. Unfortunately, Lorenzo went onto the grass slightly in Turn 1, and in the next turn he moved suddenly to get his trajectory right. He didn't see me because I was slightly behind.
"When he touched me, it pushed me into Spies, who touched my front brake lever. It was normal racing contact, but I was in the wrong place at the wrong time.
"It's a challenging time for us, but we hope we're on the right path."