The cargo of mixed oxide (MOX), a blend of plutonium and uranium, arrived at the Takahama nuclear plant on the western coast of central Japan in early morning, an AFP journalist said.
The fuel left the French port of Cherbourg in mid April bound for Japan, French nuclear group Areva has said. The vessel was specially fitted to be able to transport nuclear material and was escorted by an armed sister ship.
Dozens of anti-nuclear campaigners voiced their opposition with loudspeakers.
"We do not accept MOX fuel," a protester shouted, wearing full radiation protection gear to make his point.
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Residents of areas hosting Japan's atomic reactors are deeply divided over nuclear plants. They are often the backbone of regional economies but the memory of Fukushima remains raw two years after the world's worst nuclear accident in a generation.
Japan has few energy resources of its own and relied on nuclear power for nearly one-third of its domestic electricity needs until the meltdowns at the tsunami-crippled plant.
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 built its own nuclear fuel reprocessing plant, in northern Aomori prefecture, but its opening has been delayed by a series of minor accidents and technical problems.
This has left Tokyo dependent on other countries -- namely Britain and France -- to deal with the plutonium it has produced.
According to a government report to the International Atomic Energy Agency (IAEA), Japan has about 44.3 tonnes of plutonium, of which 35.0 tonnes are held and being processed in France and Britain, and the rest, 9.3 tonnes is stored in Japan.