Large areas of the 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.
A minor tsunami was monitored in northern Japan early on Friday after a powerful quake struck off Chile, Japanese authorities said.
A wave of 30 centimetres (12 inches) was recorded off the Japanese city of Kuji at 7:13 am (2213 GMT), the Japan Meteorological Agency.
But it way still below the possible one metre (3.3 feet) tsunami that the agency warned could hit.
Large areas of the 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.