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Considering the cost, time of construction, time saving, the project doesn't seem to make much sense. China already dropped maglev due to high cost. On the other hand, Japan is making very slow progress on cleaning up its nuclear mess and almost all of its nuclear reactors are suspended right now. Why a new railway is more important than nuclear disaster in hand?

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Remember how governments work. Transportation and energy are different budgets managed by different entities.

Not to mention that the Chuo Shinkansen will be privately financed, and is being built by a private company, JR central. They almost certainly need government cooperation (you can hardly escape that with something so huge and covering so much geographical area), but this isn't a Japanese government project, and the government isn't paying for it.

From Wikipedia: "On December 25, 2007, JR Central announced that it plans to raise funds for the construction of the Chuo Shinkansen on its own, without government financing."

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