Toyota Motor Corp. said Monday it believes the driver of a Prius involved in a high-speed incident on a California highway repeatedly pressed the brake and accelerator, apparently defeating a system that can prevent unintended acceleration.

The driver, James Sikes, has said he applied heavy pressure to the brake pedal while the car accelerated on its own last week near San Diego. Toyota said the condition of the car's brakes and information captured by the vehicle's diagnostic system don't support that version of events—even...