On April 6, 2003, during the first race of the MotoGP season at the Japanese Grand Prix held at the Suzuka Circuit, Kato crashed hard and sustained severe head, neck and chest injuries. He was estimated to have hit the wall near the Casio Triangle chicane of the circuit at around 125 mph (200 km/h).
The Accident Investigation Committee determined that Kato crashed when he lost control of his machine, which entered a near high-side state, followed by an uncontrollable oscillating weave resulting in him leaving the track and striking the barrier. Initially he and the bike struck a tire barrier, followed by a foam barrier. Importantly, there was a gap between the tire and foam barriers. Kato was fatally injured when his head struck the edge of the foam barrier, dislocating the joint between the base of the skull and the cervical spine.
Questions were raised regarding the actions of the corner workers immediately following the crash. Kato was thrown back onto the track after hitting the barriers and was lying next to the racing line. Depending on the type of race (endurance or standard), when a motorcycle and/or rider are incapacitated on the race track, a red flag is waved and the race stopped, or in endurance races and British Superbike Championship events, the safety car is called on the circuit to neutralise the race so the motorcycles are packed-up behind the said vehicle at slow speeds, so the track can be safely cleared. This did not happen following Kato's accident. Instead, the corner workers moved him onto a stretcher and off the circuit. The race was not stopped.
The Investigation Committee noted : "According to images broadcast during the race, four rescue workers took hold of Kato, who lay collapsed face up in the middle of the course, held him by the right shoulder, the torso and both legs, and moved him sideways just a few dozen centimeters onto the stretcher. It certainly appears that sufficient care was taken to immobilize his head and neck area. However, when the stretcher was moved Kato's head drooped markedly, and it cannot be denied that this might have additionally injured his neck."
Kato spent two weeks in a coma following the accident before dying as a result of the injuries he sustained. The cause of death was listed as brain stem infarction. Many of the MotoGP riders wore black armbands or placed small #74's on their leathers and bikes at the following race in South Africa to pay tribute to the fallen racer. His teammate, Sete Gibernau, has worn a #74 on his racesuit since winning the race in his memory. There has not been a Grand Prix motorcycle race held at Suzuka following Kato's crash, with safety issues at the facility being cited as the reason.