The islands were hit with moderate shaking on Monday, including one registering a magnitude 4.3, but no new reports of damage or injuries emerged, said Miyakejima island official Keizaburo Fujii.
Scientists said the earthquakes were not triggered by magma activity underneath the volcano, but urged residents to stay alert.
Tokyo Metropolitan government, which governs the island, and self-defense forces dispatched several helicopters to help.
On Sunday night, Miyakejima suffered a magnitude-6.2 quake, the strongest of tens of thousands of tremors that have hit the area since a volcano on the island started spewing up ash and steam in June.
Roads were closed as authorities began the familiar practice of disaster management on the island, which has seen an exodus of residents heading for safety on the mainland.
"The rocking was strong and items were knocked off shelves. It lasted for more than 10 seconds..." said a local reporter for public broadcaster NHK.
Earlier Sunday, an earthquake measuring 5.8 on the Richter scale jolted the same island chain, triggering landslides and causing cracks in roads. No injuries were reported.
Officials said the aftershock at 9:49 p.m. was of a magnitude of 5.4 on the Richter scale. They withdrew an earlier warning of a possible tsunami or tidal wave.
Miyakejima is one of seven islands in a chain stretching south from Tokyo that have been hit by more than 40,000 earthquakes and other natural disasters in the last month. The quakes have been triggered by volcanic activity.
The nearby islands of Niijima and Kozushima were also badly shaken on Sunday.
Earlier this month, a powerful earthquake measuring 6.4 struck Kozushima, causing landslides that killed one man -- Japan's first earthquake-related fatality in five years.
Miyakejima's volcano has erupted several times in the last few weeks, forcing the evacuation of residents living near the foot of Mount Oyama.
Many of the island's nearly 4,000 residents have already left. The string of natural disasters has decimated Miyakejima's tourism industry.
Japan is one of the world's most earthquake-prone countries as it sits atop four tectonic plates, slabs of land that move across the earth's surface.
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