The epicentre of the latest quake, which occurred at 5.16 pm local time, was in an area in Fukushima prefecture, about 164 km northeast of Tokyo, and it struck at a depth of just 10 km.
Residents in Tokyo also felt the jolts as buildings in the Japanese capital shook for nearly a minute.
After the quake, Japan's Meteorological agency issued a tsunami warning, predicting a potential tsunami wave of two-metres in Miyagi, Fukushima, Chiba and Ibaraki prefectures.
Last Thursday also, a 7.1-magnitude aftershock, which was the most powerful tremor since March 11 magnitude-9 quake and tsunami, had rattled the region, claiming four lives and leaving millions of homes without power.
Tokyo Electric Power Company (TEPCO), the operator of the Fukushima nuclear plant crippled by last month's twin disaster, temporarily evacuated its workers, who have been battling hard to stabilise the facility, after the latest quake.
Authorities also announced widening of the evacuation zone around the radiation-leaking plant due to fears of contamination, as people across the country fell silent for a minute to remember thousands of people killed last month.
"The government has designated for evacuation areas where the radiation exposure level is expected to reach 20 millisieverts per year," Chief Cabinet Secretary Yukio Edano said.
A 20-km evacuation zone was earlier put in place around the Fukushima nuclear plant after it was badly damaged in Japan's earthquake and tsunami disaster on March 11.