Fires broke out after the initial 6.4 magnitude jolt, including a smoky blaze at a textile factory in the southern city of Tainan.
Power was knocked out and high-speed rain lines were suspended while crews checked for damage.
The epicenters of the quakes were near the mountainous town of Jiashian, which was ravaged by Typhoon Morakot’s fury last August.
The shaking was felt across all of the island of Formosa at 8:20 a.m. local time, including in Taipei and Kaohsiung where tall buildings swayed for about a minute.
Some residents in southern Taiwan reported being trapped in elevators due to the loss of power.
Four years ago, a 6.7 magnitude temblor centered beneath the Pacific Ocean off Taiwan severed undersea cables and disrupted telephone and Internet service throughout Asia.
A 7.6-magnitude quake in central Taiwan in 1999 killed more than 2,300 people.