The 27-year-old told Autosport: "We just made a mistake and now we are stuck with it.
"I felt we had a great car all weekend, it was just the setup changes and then the car would not turn anymore. We were miles off and when you start you first lap you think 'damn, I wish I had gone the other way.'"
Hamilton believes that he will struggle to pick up places in the race.
The race gets underway at Suzuka tomorrow at 7am UK time, with reigning world champion Sebastian Vettel on pole.