The strongest of Monday’s tremors measured 5.0 on the Richter scale, though no casualties or major damage were immediately apparent, Reuters reported.
But about 500 people were injured in Saturday's quakes in the Miyagi prefecture, 300 km north of Tokyo. The tremors also triggered landslides and power cuts.
Some 2,500 people spent Sunday night in public shelters, local press reported. At least six homes were completely ruined and some 900 houses partially destroyed. More than 200 aftershocks were felt in the region earlier in the day.
Electricity had been restored by Monday to about 100,000 households affected by the quakes, and key transport routes were operating normally, according to the Japan Times. But disruptions in water services continued at some 12,000 households.
The first earthquake on Saturday, measuring 5.5 on the Richter scale, hit shortly after midnight, followed by another measuring 6.2 about seven hours later.
Residents in Miyagi expressed anxiety amid the continuing tremors.
"How long will these earthquakes last? It's frightening really," one elderly woman told local broadcaster TV Tokyo at a school in the small town of Nango, where evacuees were wrapped in blankets.
Saturday was the first time since 1949 that a series of high magnitude tremors occurred consecutively, the Japan Times said.
But it quoted meteorological officials saying Saturday's quakes are apparently not linked to the so-called Miyagi-oki earthquake, which has hit the region cyclically every 30 to 40 years. It last struck in 1978, killing 28 people.
Japan is one of the world's most earthquake-prone countries. In 1995, a strong quake hit the city of Kobe 435 km west of Tokyo, killing nearly 5,000 people and injuring 15,000.