Many social media users reacted to the company's apology with surprise.
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It added that no customers had complained about the early departure from Minami Nagareyama Station, which is just north of Tokyo.
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 Tokaido 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.
Impressed railway users worldwide tweeted the story to their local train operators - particularly in Britain, where rail services are often delayed.
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