The quake's epicentre was in the town of Jiashian in the mountainous region about 70 kilometres northeast of the industrial city of Kaohsiung, the Central Weather Bureau said.
The bureau said the quake was the biggest to hit the Kaohsiung area in recent years.
Local media reports said residents in Kaohsiung rushed out into the streets as buildings started shaking, and were reluctant to re-enter.
The US Geological Survey put the quake's magnitude at 6.4, revised from an initial 6.5 and put the depth at five kilometres.
Liang Yu-chu, a spokesman with Taiwan's National Fire Administration disaster response centre, said the quake set off five fires, including one at a textile factory, and caused several incidents of elevators becoming jammed in their shafts.
Ling added that no major damage was reported near the epicentre, a rural area hard hit in August by Typhoon Morakot, a powerful storm that left about 700 people dead.
Officials in the southern county of Chiayi reported some objects falling off rooftops.
In Nantou, another city in the island's south, water and power lines were cut.
Taiwan is regularly hit by quakes as the island lies near the junction of two tectonic plates.
One of the island's worst-recorded earthquakes measuring 7.6 occurred in September 1999.
More than 2,400 people were killed in the disaster, which damaged or destroyed some 50,000 buildings.