A 5.9 scale earthquake struck a remote area further north in the Pacific Ocean, which caused no immediate reports of damage.
A wave of 50cm reached Hachijo area, one of the Izu archipelago, about 40 days after the disaster, according to the Japan Meteorological Agency.
No harm from the storm or the disaster has been confirmed, public journalist NHK reported.
People of the Izu and Ogasawara territories must be prepared for a storm as high as 1m hitting the beach, according to the weather company.
The agency added that since the disaster struck beneathsea near the sparsely populated Torishima area about 600 kilometers north of Tokyo, no significant tremors have been found.
The Izu islands, along with the yet more isolated Ogasawara islands further south, have about a dozen inhabited islands and a combined population of about 24, 000 as of last year, according to the Tokyo Metropolitan Government, which covers the parts.