It said a 40cm (16 inches) wave hit Nemuro port in Hokkaido island. Another one of 20cm (8 inches) was recorded.
The JMA initially expected a tsunami of at least two metres (6.5 feet) high after an 8.1 magnitude earthquake shook the Kuril Islands, north of Japan.
Tsunami warnings for the area and for Russia's Pacific coast were later called off.
Island threat
The earthquake struck about 390km (240 miles) east of Iturup, known as Etorofu in Japan, at 2015 (1115 GMT), the JMA said.
There have been no reports of injuries or damage following the earthquake.
The BBC's Chris Hogg in Tokyo says in the past tsunamis have caused extensive damage in Japan but they were of a far greater magnitude than is being predicted.
Japan's precarious geological position makes it one of the world's most earthquake-prone nations.
As such, it has developed a sophisticated tsunami warning service, run by the JMA.
If an earthquake looks as if it has the potential to trigger a tsunami, the JMA issues an alert within three minutes of it being identified.
The tsunami alert issued for certain areas of Russia and Japan after an 8.1 magnitude earthquake struck near the north coast of Japan have been lifted. While the tsunami alert has been lifted, Japan's Meteorological Agency's web site is still showing watches in affect for most of the eastern Pacific coast of Hokkaido.

A small 40cm (15.7 inches) wave did wash up in some areas of the eastern coast of Japan, but this was nowhere near the 200cm (6.5 feet) wave that had been feared.