A government press release said the International Seabed Authority (ISA) had approved Japan's plan to probe a 3,000-square-kilometre area beneath international waters off the isolated Japanese coral atoll of Minamitorishima.
The area is located 600 kilometres off the atoll which lies 1,850 kilometres south of Tokyo.
The Japan Oil, Gas and Metals National Corporation, acting on the government's behalf, is due to sign a formal contract with the ISA covering 15 years of exploration rights, the statement said.
Resources-poor Japan needs the metals for its high-tech components, including lithium-ion batteries and automobile engines.
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China, the world's leading supplier of rare metals and rare earths, has used its position as diplomatic leverage at a time when it is locked in a row with Japan over Tokyo-controlled islands in the East China Sea.
In 2010, China restricted rare-earth exports when Japan arrested the captain of a Chinese trawler that was involved in a run-in with two Japanese coastguard cutters trying to coax it away from the disputed Senkaku Islands, claimed by China which calls them Diaoyu.
Japan last obtained exclusive rights to explore the seabed for minerals under international waters in 1987, for manganese nodules in an area southeast of Hawaii, the statement said.