A tsunami surge of 80 centimetres (32 inches) was recorded off the northeast coastal city of Kuji at 9:38 am (0038 GMT), the Japan Meteorological Agency said, while smaller waves also hit other areas.
Local television showed no visible damage to Japanese coastal regions from the aftermath of a huge 8.3-magnitude earthquake that killed at least 11 people in Chile and ravaged long stretches of the coast.
"At this level of tsunami we don't have to worry that the land will be inundated, but underwater current could be very strong and you may be washed away," he said.
Public address systems all along the coast broadcast warnings, while emergency vehicles patrolled with their sirens blaring, to keep away from the shore.
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Authorities have warned of waves up to one metre (3.3 feet) high, although none have yet been reported, and Chief Cabinet Secretary Yoshihide Suga told reporters the government had not received reports of any damage.
"But we keep calling on our residents to stay away from the coast for now," he told AFP.
Large areas of Japan's coastline -- including Kuji -- covered by the agency's advisory were wiped out by the 2011 quake and tsunami, which triggered a nuclear accident in Fukushima.
The 9.0 undersea quake set off a massive tsunami that swamped cooling systems at the Fukushima Daiichi power plant, sparking the worst atomic accident in a generation.
The Chilean quake struck offshore north of the capital Santiago on Wednesday evening, killing at least 11 and triggering tsunami waves that ravaged stretches of the coast.