A Japanese rail company has apologised profusely after a train accidentally left 25 seconds ahead of schedule.

The West Japan Railways train left Notogawa Station bound for Nishi Akashi at 35 second past 7:11am on Friday morning (local time) instead of the scheduled 7:12am.

The conductor realised his mistake when he closed the doors at 7:11, one minute early - but thought there was no one at the station, so left early.

However, there were passengers out of his sight who were planning to board the train.

"The great inconvenience we placed upon our customers was truly inexcusable," West Japan Railways said in a statement.

"We will be thoroughly evaluating our conduct and striving to keep such an incident from occurring again."

The next train to leave Notogawa for Nishi Akashi was at 7:19am, just 8 minutes later.

Newshub.