The strongest of more than 200 tremors was measured at 6.1 by the USGS as shaking continued through the night.
Taiwan has been rattled by a cluster of dozens of earthquakes that caused buildings to sway and that the government said were aftershocks from the huge quake that hit the island more than two weeks ago.
The strongest of the latest tremors, which the United States Geological Survey measured at a magnitude of 6.1, hit at about 2.30am (18:30 GMT) followed minutes later by a 6.0 tremor.
Taipei’s Central Weather Administration put them at 6.0 and 6.3, respectively.
The seismic activity, which was centred around Hualien on the east coast, caused buildings across large parts of northern, eastern and western Taiwan to shake throughout the night. There were no reports of casualties.
Office worker Kevin Lin, who lives in the capital Taipei, told the AFP news agency that the quake woke him.
“I was too scared to move and stayed in bed,” the 53-year-old said.
At about 8am (00:00 GMT), a 5.8-magnitude tremor shook the capital as commuters made their way to work.
The mountainous county of Hualien, about 150km (93 miles) from Taipei, was the epicentre of a magnitude-7.2 quake that struck the island on April 3, severely damaging buildings in Hualien City and triggering landslides in the surrounding countryside.
At least 14 people were killed, and there have been more than 1,100 aftershocks.
Taiwan’s Central Weather Administration said the latest cluster of earthquakes were also aftershocks.
Seismological Centre Director Wu Chien-fu told reporters that the quakes were a “concentrated release of energy” and that more could be expected, although perhaps not as strong.
In Hualien, the government announced that schools and offices would remain closed on Tuesday due to the continuous aftershocks.
Buildings that partially collapsed in the April 3 quake, including the Full Hotel and the nearby Tong Shuai Building, were further damaged. Both were empty and have already been marked for demolition.
The April 3 quake was the most serious in Taiwan in 25 years, but the toll was relatively contained thanks to widespread public awareness campaigns and stricter building standards.
The island of 23 million people lies near the junction of two tectonic plates and is no stranger to powerful earthquakes.