The green, pink and silver train is the fastest currently operating in Japan, travelling at speeds of 198mph.
Japan has built up a network of high-speed rail lines since the 1960s that criss-cross the island nation.
It now hopes to sell the technology abroad, including to the United States.
Mutsutake Otsuka, chairman of East Japan Railway Co, said: "To the best of our ability, we will strive to improve Hayabusa's passenger comfort, safety and environmental friendliness, not just its speed."
More than 1,000 train spotters crowded on to the platform at Tokyo's central railway station to see the futuristic train leave.
It can make the 420mile trip to Aomori in just over three hours.
Passengers will glide quietly along the straight stretches and tunnels that cut through Japan's mountainous countryside.
And those willing to pay 26,360yen (?196) for a one-way trip can enjoy the comfort of a Gran Class car, where a cabin attendant will serve them food and drinks in their deeply reclining leather seats on thick woolen carpets.
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