On Friday, the train's driver thought he was slated to leave Notogowa station at 7.11 am instead of the actual scheduled time of 7.12am and closed the doors, BBC quotes Japan Today.
Instead of fixing the mistake and re-opening the doors, the driver left the station at 7.11:35 - a massive 25 seconds early - as he couldn't spot any passengers on the platform.
According to Sydney Morning Herald, one person missed their train on Friday because of the driver's error of judgement. The person complained to the station in-charge who took the very serious matter to higher authorities, reports Independent.
The company quickly came forward to do damage control.
The company added that they would provide training to prevent similar events in the future.
Japan prides itself on its punctual train services. In November last year, a Japanese railway operator issued a deep apology for the "tremendous nuisance" caused by a train that departed 20 seconds early.
The Tsukuba Express train linking Tokyo and the capital's northern suburbs pulled out of Minami Nagareyama Station at 9:44:20 instead of 9:44:40. Click for more trending news