TOKYO—Japan has hundreds of years’ worth of rare-earth metal deposits in its waters, according to new research that reflects Tokyo’s concern about China’s hegemony over minerals used in batteries and electric vehicles.

The deposits were found in the Pacific Ocean seabed near remote Minamitori Island, about 1,150 miles southeast of Tokyo. Extracting them would likely be costly, but resource-poor Japan is pushing ahead with research in hopes of getting more control over next-generation technologies and weapon systems.

A...