A magnitude 6.7 earthquake hit the region most affected by the March 11 magnitude 9.0 quake and tsunami.
The strong jolt hit at 6:51 am local time, 31 miles off the coast of Miyako, Iwate prefecture.
A tsunami warning was issued but no high waves were reported. No tsunami warning was issued for the Fukushima nuclear plant.
There are no immediate reports of earthquake damage.
Japan issued a tsunami warning Thursday after a magnitude-6.7 earthquake struck in the northeast of the country, rattling the areas hardest hit by the March 11 quake and tsunami disasters.
But the meteorological agency lifted the warning about an hour after the latest jolt hit at 6:51 am (2151 GMT Wednesday) some 50 kilometers (31 miles) off the east coast of Miyako, Iwate prefecture, at a depth of 20 kilometers in the Pacific.
USGS also registered the quake at 6.7 in magnitude at a depth of 32 kilometers.
The Japanese agency had warned that a 50 centimeter (20-inch) tsunami could be expected in the region, but no warning was issued to Fukushima at the center of the nation's nuclear crisis.
Public broadcaster NHK reported there were no immediate reports of damage from the quake while no sizable high waves were seen.
Local authorities issued evacuation orders to some 8,000 households in Iwate, NHK said.
Shinkansen bullet train services were temporarily suspended, while there was no new damage to the Onagawa nuclear power plant in Miyagi, south of Iwate, which has been out of operation since the March 11 disaster, NHK added.
The northeast coast of Japan's main Honshu island was ravaged by a 9.0 magnitude quake and monster tsunami on March 11 which left some 23,000 people dead or missing.
The disasters also crippled the Fukushima Daiichi nuclear power plant, triggering the world's worst atomic accident since Chernobyl in 1986 and forcing hundreds of thousands of residents to leave their homes.