Fears that the tiny uninhabited island, known as Esambe Hanakita Kojima, was washed away has prompted plans for a survey of the area.
Until recently, it rose 1.4m (4.5ft) above sea level, and was visible from the very northern tip of Japan’s northern Hokkaido island.
“It is not impossible that tiny islands get weathered by the elements,” a coastguard official said.
It was only officially surveyed and registered in 1987 by Japan’s coastguard which was unable to confirm the island’s size.
If it has disappeared, the country’s territorial waters will shrink.
The disappearance of the island “may affect Japan’s territorial waters a tiny bit… [but only] if you conduct precision surveys,” the official added.
Japan invests in protecting its outer islands, particularly the remote Okinotori islands in the Pacific, and is locked in disputes with neighbours, including China and South Korea, over the sovereignty of several islands.
The small islands are guarded by Japan in an effort to clarify its territory and extend its exclusive economic zone.
Prone to earthquakes and severe weather, Japan has sometimes gained territory as well as losing it.
In 2015, a 300-metre strip of land emerged from the sea and attached itself to the coast of Hokkaido.
Geologists said it was probably the result of a landslide that pushed the underwater surface up.
In 2013, a volcanic island appeared around 620 miles 1,000km) south of Tokyo, engulfing an existing island and continuing to grow.