The deceased has been identified as Kiran Sapkota, 30, of Baglung municipality-6 while the details of the seriously injured are yet to be ascertained.
Though the incident took place on Tuesday afternoon, the police had disclosed the death late on Wednesday only.
Sapkota had entered Japan on cook visa two years back. He was returning home from a Nepali restaurant at Khanajava city when the incident took place.
The injured is said to be a close relative of deceased Sapkota, according to police.
A speeding car with unidentified number plate had knocked them from back at a local road in Raimaru town, which is in the south from capital city Tokyo.
The local Hansosaki Hospital, where he was undergoing treatment, had declared Sapkota dead immediately after the accident.
Police said they are carrying out serious investigation into the incident.
Injured duo, car driver and relative of Sapkota are being treated in the hospital, police informed.
No Nepali society in Japan has made any official remarks regarding the incident.