The quake also shook buildings in the capital Taipei. Authorities said subway services in the city continued at lower speeds.
"It was close," said Hsieh Yu Wei, a singer who pulled his car over the moment he received a government-issued quake warning while driving on a Hualien coastal highway.
The quake had a depth of 9.7 km, the weather administration said, and followed a 5.7 magnitude earthquake that struck off Taiwan's northeastern shore on late Thursday.
Weather officials warned of aftershocks that could reach a magnitude of 5.5 in the next few days. Around a dozen earthquakes were recorded near Hualien since the major tremor this morning.
Weather officials have warned of the risk of landslides in mountainous areas following days of rain.
Taiwan lies near the junction of two tectonic plates and is prone to earthquakes.
In April, Hualien was hit by the biggest earthquake to affect Taiwan in at least 25 years. Nine people were killed and more than 900 injured.
