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.
A tsunami warning has also been issued for Russia's Pacific coast by the US Pacific Tsunami Warning Center.
Warnings are being broadcast on all Japanese TV and radio stations advising people to move to higher ground.
The earthquake struck about 390km (240 miles) east of Iturup, known as Etorofu in Japan, at 2015 (1115 GMT), the JMA said.
The US Pacific Tsunami Warning Center said the tsunami warning also applied to Marcus island, Wake island and Midway island.
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.Güncelleme Tarihi: 20 Eylül 2018, 18:16