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.
"We deeply apologise for causing tremendous nuisance to customers," said the Tsukuba Express company.
"There was no complaint from customers over this incident," said the firm, which added that no one missed the train due to the early departure.
Japanese railway services, including shinkansen bullet trains, are famous for their world-beating punctuality.
Even the slightest delay prompts an effusive apology from the train guard, which often lasts longer than the hold-up itself.
With trains running the same route every few minutes to cope with huge numbers of passengers, even brief delays can back up the whole network causing overcrowding.
The apology had several social media users scratching their heads.
"A weird country in which a 20-second difference prompts a sincere apology while faking quality data on aluminium and steel products or misconduct on car check-ups are done just like that," read one tweet.
This was a reference to a recent string of corporate scandals that has floored the reputation of Japan Inc.
Car giants Nissan and Subaru have admitted that uncertified staff had inspected vehicles while Kobe Steel has been embroiled in a quality data-faking scandal.
