There has been no major physical damage on hardest-hit Akuseki island, even after a 5.1-magnitude quake that struck overnight, said Genichiro Kubo, who is based on another island.
But the almost non-stop jolts since June 21 have caused severe stress to area residents, many of whom have been deprived of sleep.
Of the 89 residents of Akuseki, 44 have evacuated to the regional hub of Kagoshima by Sunday, while 15 others also left another island nearby, Kubo told a news conference.
The municipality, which comprises seven inhabited and five uninhabited islands, is roughly 11 hours away on a ferry from Kagoshima.
Since June 21, the area has experienced as of early Monday what seismologists refer to as a swarm of 1,582 quakes.
Experts have said they believe an underwater volcano and flows of magma might be the cause. They say they cannot predict how long the tremors will continue.
"We cannot foresee what might happen in the future. We cannot see when this will end," mayor Kubo told reporters.
A similar period of intense seismic activity in the area occurred in September 2023, when 346 earthquakes were recorded, according to the Japan Meteorological Agency.
Japan is one of the world's most seismically active countries, sitting on top of four major tectonic plates along the western edge of the Pacific "Ring of Fire".
The archipelago, home to around 125 million people, typically experiences around 1,500 jolts every year and accounts for about 18 percent of the world's earthquakes.
Some foreign tourists have held off coming to Japan due to unfounded fears fanned by social media that a major quake was imminent.
Causing particular concern was a manga comic reissued in 2021 which predicted a major disaster on July 5, 2025 -- which did not happen.
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