Typhoon Hagibis crashed into the country on Saturday night, unleashing high winds and torrential rain across 36 of the country's 47 prefectures, and triggering landslides and catastrophic flooding.
Typhoon Tapah was passing near Nagasaki in southern Japan on Sunday afternoon after hitting other parts of southern Japan, including Okinawa, the two previous days.
The quake jolted large areas in the region at 7:23 pm (1023 GMT) with its epicentre located 54 kilometres (34 miles) east of Namie, eastern Fukushima, according to the US Geological Survey said.
Rescue helicopters and boats plucked more people from their homes in the Kumamoto region. Up to 10,000 defense troops, the coast guard and fire brigades are taking part in the operation.
The epicentre of the earthquake was 41.7 kilometres beneath the Pacific seabed, less than 50 kilometres off the coast of Miyagi prefecture, the USGS said on its website, rating the risk of casualties and damage as low.
More than 300 people, including hotel employees and visitors, were trapped in Kamikochi, as floods and mudslides hit a main road connecting the town to Matsumoto, another tourist destination in Nagano.
Japanese Minister for Foreign Affairs Toshimitsu Motegi has praised the launch of the United Arab Emirates’ Hope Probe to Mars, noting that it is a "very important project" symbolising the "strong relationship" between the two countries.
The Japanese Meteorological Agency had said earlier that Maysak was expected to later make landfall on Kyushu, Japan’s main southern island, but its course appeared to be swerving away. Still, its passing close by could bring strong winds and rain.