The joint declaration pledges to deepen and accelerate ties in the research and development of next-generation nuclear such as sodium-cooled fast reactors.
Work will continue on the safe life extension of existing reactors, decommissioning of nuclear plants including Japan's Fukushima Dai'ichi reactor, developing civil nuclear capacity in interested countries, and promoting the recycling of used nuclear fuel to minimize the need for uranium.
French Energy Minister Agnes Pannier-Runacher met Nishimura Yasutoshi, Japan's minister of trade, economy and industry and they discussed accelerating technical cooperation on the nuclear fuel cycle, and working to build a supply chain involving only countries sharing "common values".
The announcement followed talks on the sidelines of the Group of Seven energy and climate meeting in Sapporo last month, where the ministers discussed cooperating on a relaunch of nuclear energy in Japan as a way to meet rising power demand without a spike in greenhouse gas emissions.
"The new flags of this bilateral Franco-Japanese partnership, the Tricolor and the Hinomaru rising sun, wave strongly toward decarbonisation and a stable energy supply," Nishimura said in a statement.
The joint declaration came a day after a Paris appeals court allowed the French government to proceed with a buyout of nuclear giant EDF as part of its long-term plan to reinvigorate the nuclear sector and build up to 14 new reactors by 2050.
France this year also signed a bilateral agreement with Britain emphasising nuclear as a low-carbon energy source that could reduce dependence on suppliers like Russia.