Nicky Hayden said he had no warning that Yuki Takahashi was even approaching when the Japanese rookie ran into him on the first lap at Motegi.
Both riders were taken out of the race in the collision, which saw Takahashi's Scot Honda hit the back of Hayden's factory Ducati.
"That was exactly what we didn't need," said Hayden. "I got a decent start and I think I was up a couple of positions but just going down into the hairpin, which is a slow hard-braking corner, I was on my line and Takahashi just took me down.
"There was no warning - I didn't even hear anything! I don't want to say much about that, I don't want to look like a cry-baby but, you know, it was the first lap..."
Takahashi apologised for the incident, but could not offer an explanation.
"I was in a group of drivers, more or less all of us at the same speed, then the collision under braking," he said. "I'm really sorry. Out at the very beginning of the race - what a pity. Not only for the race itself, but especially because I need laps to learn and improve."
The crash came just a fortnight after Hayden's ferocious high-side in Qatar qualifying, but the American escaped injury - and remained optimistic about his progress with the hard-to-master Ducati GP9.
"Luckily I feel okay," he said. "I actually landed in the same place on my back as the crash in Qatar and my leathers and helmet have got exactly the same marks.
"It's a shame because this weekend I honestly felt we were making some progress. I felt we had better communication going on and we worked more comfortably from the first day.
"I know we were never looking at a great result but I felt I could have been competitive today. Anyway, we have to move forward and to look to the next race."