Management on the Tsukuba Express line between Tokyo and the city of Tsukuba said they "sincerely apologise for the inconvenience" caused.
In a statement, the company said the train had been scheduled to leave at 9:44:40 local time but left at 9:44:20.
The mistake happened because staff did not check the timetable, the statement said.
"The crewman handled the passengers on board after opening the door. After that... I closed the door without checking the departure time sufficiently," it said.
No customers had complained about the early departure from Minami Nagareyama Station, which is just north of Tokyo, the statement added.
The Tsukuba Express line takes passengers from Akihabara in eastern Tokyo to Tsukuba in about 45 minutes.
It is rare for trains in Japan, which has one of the world's most reliable railways, to depart at a different time to the one scheduled.
The country's Tokkaido line, which runs from Tokyo to the city of Kobe, is by far the world's busiest and carries nearly 150 million passengers a year.