The Foreign Ministry said a bilateral civil nuclear cooperation accord with Russia will take effect May 3, providing all necessary procedures have been completed.
The pact will pave the way for domestic companies to export nuclear technologies to Russia and help Japan secure uranium enrichment services from the energy-rich country.
The validity of the accord, signed by Japan and Russia in 2009, was confirmed by Foreign Minister Koichiro Genba and Sergei Kirienko, head of Russia's Nuclear Energy State Corporation (Rosatom), during a meeting in Tokyo on Tuesday.
The pact was approved by the Diet in December with the support of both ruling and opposition lawmakers, although concerns remain over the safety of nuclear energy in light of the Fukushima crisis.
Kirienko told reporters after the meeting he is ready to cooperate with Japan in the disposal and decontamination of rubble and waste that remain in the vicinity of the wrecked Fukushima No. 1 power plant.
The Rosatom chief, who visited the plant Monday and met with officials of Tokyo Electric Power Co., said the disaster is a "tragedy" for Japan and for other countries that rely on nuclear power.
He said that Russia's experience of dealing with the 1986 Chernobyl disaster in what was then the Soviet republic of Ukraine could prove useful in handling the Fukushima nuclear crisis.