Removal of the melted rods at the nuclear plant, which was wrecked by a tsunami five years ago, is one of the biggest challenges of the mammoth cleanup, a huge project expected to take up to four decades.
Scientists have long warned the technology required for the complex -- and potentially dangerous -- task does not yet exist, and would have to be invented.
Entombing the uranium rods in concrete and effectively abandoning the site -- as was done after the meltdown at Chernobyl in 1986 -- has been ruled out by the Japanese government as politically unacceptable, leaving innovation as the only possible solution.
Japan's science and technology ministry said it would work with the US Energy Department and the French National Research Agency on the project -- a key step towards eventual decommissioning, which is expected to begin in 2021.
"This is the first basic research led by the government designed to help decommission Fukushima Daiichi after TEPCO worked together with its partners overseas at the private level," a ministry official said, referring to the operator of the plant.
Under the plan, the US side will help Japan develop equipment and technology to manage and dispose of highly-radioactive waste produced from the decommissioning work, the official said.
France will cooperate with Japan in developing remote-control technology, including robotic and image processing expertise that can withstand high-radiation environments, he said.
The Japanese government plans to finance the projects by spending part of its "Fukushima technology development budget" worth 25 billion euros.
Japan last week marked five years since an offshore earthquake sent a huge tsunami crashing into its northeast coastline.