The wave was recorded in Ishinomaki, a city in Miyagi prefecture that was badly hit by the tsunami of March 2011, which killed thousands.
A magnitude-7.3 earthquake struck north-eastern Japan earlier on Friday, and the meteorological agency had issued a tsunami warning for coastal areas.
No damage or injuries were immediately reported from the quake, which was centred off the prefecture at a depth of 10 kilometres, the agency said.
The region was struck on March 11, 2011, by a magnitude-9 quake, which caused major damage and set off a tsunami that devastated coastal communities.
About 18,600 people died or went missing in the disaster.
No abnormalities were observed on Friday at the Fukushima Daiichi Nuclear Power Station in Fukushima prefecture, which borders Miyagi, its operator, the Tokyo Electric Power Co, said.
The plant went into meltdown after it was hit by the March 2011 disaster and has been shut down ever since.
The number of people who died or went missing in the March 2011 tsunami