A 50-centimetre tsunami hit an island south of Tokyo on Tuesday after a 5.9-magnitude earthquake struck the region.

The Japan Meteorological Agency issued a tsunami warning for the islands of Izu and Ogasawara immediately after the quake.

The epicentre of the quake was in the waters near Torishima, in the Izu island chain in the Pacific Ocean, about 10 kilometres under the surface.

The agency predicted a tsunami of up to one metre high and urged people to stay away from coastal areas.