A magnitude-6.8 earthquake first struck the southern coast of Hokkaido island in the evening, causing a small tsunami. Tsunami advisories were issued along the northern Pacific coast, prompting some communities to advise residents to evacuate coastal homes.
A swelling of 20 centimeters (8 inches) was observed in water at the port of Hachinohe in Aomori about an hour after the tremor, with smaller changes reported elsewhere. The agency lifted all tsunami advisories within about 90 minutes.
Within about three hours, a magnitude-6.1 quake shook buildings in the capital. It was centered just off the coast of Chiba, east of Tokyo, at a rather shallow 15 kilometers (9 miles) below the sea surface.
Narita International Airport briefly closed runways for inspection but later resumed operation. Several local train services were suspended for safety checks.
There were no abnormalities reported at nuclear power plants after the two earthquakes, operators said. Nearly all of Japan's nuclear plants are offline for safety inspections.
This past Sunday, Japan marked the first anniversary of the massive magnitude-9.0 earthquake and tsunami that left some 19,000 people dead or missing, wreaked widespread damage along the northeastern coast, and triggered the worst nuclear accident since Chernobyl. Rebuilding has yet to fully begin in many coastal communities.
The temblors were considered aftershocks of last year's massive quake, Meteorological Agency official Akira Nagai told a news conference, warning residents to stay away from buildings and plots already loosened by that tremor and the thousands of aftershocks that have followed.
After the first quake on Wednesday, the town of Otsuchi in Iwate prefecture, where more than 800 died in last year's tsunami, issued an evacuation order to coastal households as a precaution, said prefectural disaster management official Shinichi Motoyama. No damage or injury was reported, he said.
Iwate was heavily damaged by last year's tsunami. Nearly all of the thousands of aftershocks since then have been of minor or moderate strength.