The major focus for emergency responders remained the Yun Tsui apartment block where the majority of the deaths occurred and dozens are still missing.
The lower floors of the 12-storey tower -- which also housed a hotel -- pancaked, leaving the structure leaning at a fifty-degree angle and sparking fears of an imminent collapse.
Despite those risks rescuers kept going into the building throughout Wednesday night and Thursday morning in a desperate search for survivors.
Strong aftershocks coursed through the ground sending rescue teams running from the building, only for them to return a little while later and resume their grim task.
One aftershock shortly before midnight on Thursday measured 5.7-magnitude.
Chu Che-min, the Hualien fire department's rescue team leader at the scene, told AFP they located two more bodies overnight.
"We discovered the body of a Chinese woman at the hotel in Yun Tsui (building) earlier this morning and located another person who's a hotel staffer," he said.
In a updated toll, the national fire agency said nine people had now been confirmed killed in the quake including three Chinese mainland nationals.
The three mainland victims were all believed to be staying at the Beauty Stay Hotel, which was located on the second floor of the apartment block.
At least 62 people remain unaccounted for across the city. In the apartment block, 37 people are missing from flats alongside 10 hotel guests. More than 250 people were injured in the tremor, the strongest to hit Hualien in decades.
Hualien is one of Taiwan's most popular tourist hubs as it lies on the picturesque east coast rail line and near the popular Taroko Gorge.
But the mountains that rise up behind the city -- and bestow Taiwan's east coast with such majestic beauty -- are a testament to the deadly tectonic faultlines that run through the island.
The government said 17 foreigners sought medical treatment for minor injuries.
Local broadcaster SET TV ran an interview with a man who said he was the husband of one of the Chinese mainland victims.
The woman, named as 39-year-old Yu Fei, was travelling with the couple's young son on the island. The son survived the quake with light injuries. She was pulled from the wrecked building and later died in hospital.
"They were travelling on their own as I was busy and couldn't accompany them," the man, who had rushed from the mainland Chinese city of Xiamen, said. "I got in touch with my son, he cried. I haven't seen him in person."
President Tsai Ing-wen, who visited survivors on Wednesday and the Yun Tsui apartment block, praised emergency responders.
"Rescuers on the scene and hospital staffers continue to dedicate themselves fully to the rescue works," she wrote on Facebook."Stay hopeful and never give up."
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