The controversial shipment from a plant of the French nuclear group Areva located some 20 kilometres (12 miles) away arrived at the port before dawn aboard two trucks escorted by dozens of security vehicles as a helicopter flew overhead.
Around 20 Greenpeace activists carried protest banners and threw smoke bombs at the convoy shortly before it arrived at the port.
It is the sixth shipment of mixed oxide (MOX), a blend of plutonium and uranium, from France to Japan since 1999.
Areva spokesman Alexandre Marinot described the cargo as being of "a maximum safety level."
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Uranium reactors produce a mixture of depleted uranium and plutonium as a by-product of fission. These can be re- processed into MOX fuel, which can then be used in other reactors to generate more power.
Japan has few energy resources of its own and relied on nuclear power for nearly one-third of its domestic electricity needs until the 2011 meltdowns at the tsunami-crippled Fukushima plant.
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