The quake hit near Torishima island, some 600 kilometres south of Tokyo, at 1:51 am (local time Sunday), the weather agency said.
Following the quake which hit a very shallow point of the seabed, the agency issued a tsunami waring of up to one metre (3.3 feet) for the Izu island chain, south of Tokyo, and the Ogasawara archipelago, far south in the Pacific Ocean.
A wave of 50 centimetres was seen to have reached Hachijojima island, one of the Izu islands, the agency said.