The warning was issued after a magnitude 7.3 quake struck offshore at 8.18am UK time, swaying buildings across much of Japan. There were no immediate reports of serious damage but two people were reportedly hurt.
After the quake, authorities issued a warning that a tsunami potentially as high as 8ft could hit. Ishinomaki, a city in Miyagi, reported that a tsunami of 4ft hit at 9.02am UK time. About two hours after the quake struck, the tsunami warning was cancelled.
The earthquake struck in the Pacific Ocean off the coast of Miyagi prefecture, the meteorological agency said. The epicentre was 6.2 miles beneath the seabed and 150 miles offshore.
The area was shaken by smaller aftershocks, the agency said.
Japan has barely begun to rebuild from last year's magnitude-9.0 earthquake, which triggered a tsunami that swelled to 65ft high in some areas, ravaging dozens of coastal communities in Miyagi and elsewhere. About 19,000 people were killed and some 325,000 people remain displaced from their homes, living in temporary quarters.
Miyagi prefectural police said there were no immediate reports of damage from yesterday's quake and tsunami, although traffic was being stopped in some places to check on roads.
Public television broadcaster NHK reported that five people were injured, including a 75-year-old woman in Miyagi who fell while fleeing the tsunami. Police said they could not immediately confirm those reports.
Shortly before the earthquake struck, NHK broke off regular programming to warn that a strong quake was due to hit.
The meteorological agency has an early warning system that enables it to provide advance warning of the estimated intensity and timing of a major quake.
Immediately following yesterday's quake, there were no problems at any of the nuclear plants operated by Tokyo Electric Power Co, said a Tepco spokesman.