The fuel was due to leave the northern French port city of Cherbourg earlier this month but was delayed by the breakdown of loading equipment.
Environmental activists have denounced the practice of transporting such highly radioactive materials, calling it irresponsible.
The previous transport of MOX fuel to Japan in September 2021 drew protests from environmental group Greenpeace.
MOX fuel is a mixture of reprocessed plutonium and uranium.
"The Pacific Heron and Pacific Egret, the specialised ships belonging to British company PNTL, left Cherbourg harbour on September 17. They will ensure the shipment of MOX nuclear fuel to Japan," French nuclear technology group Orano said in a statement Saturday.
They are bound for Japan for use in a power plant and Orano said it expected the shipment to arrive in November.
Japan lacks facilities to process waste from its own nuclear reactors and sends most of it overseas, particularly to France.
The operation was carried out "successfully", Orano said, and it is the second shipment that arrived in Cherbourg from a plant in La Hague, located 20 kilometres (12 miles) away, after the first came on September 7.
Yannick Rousselet of Greenpeace France previously denounced the shipment.
"Transporting such dangerous materials from a nuclear proliferation point of view is completely irresponsible," he said last month.
MOX is composed of 92 percent uranium oxide and eight percent plutonium oxide, according to Orano.
The plutonium "is not the same as that used by the military," it said.
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