He had asked a conductor, who did not have a driver's licence, to man the train which was travelling at 150km/h (93mph), according to local media.
The Hikari 633 was carrying 160 passengers at the time. The incident reportedly did not affect the journey.
But the railway company has reported it to authorities and apologised.
The Central Japan Railway Company (JR Central) said the incident took place on Sunday morning while the train was travelling in the central Shizuoka prefecture.
