Across the island, around 20,000 homes were still without power Saturday, mostly in the worst-hit southern seaport city of Kaohsiung, where the typhoon made landfall.
Krathon dissipated into a tropical depression on Friday after slamming into the island the day before, bringing mudslides, flooding and record-strong gusts.
More than 700 people were injured.
On Saturday, two missing people were found dead in northern New Taipei city, bringing the typhoon's death toll to four, the National Fire Agency said without providing details.
Heavy rains triggered landslides in several districts of New Taipei and flooded streets, temporarily stranding dozens of students at their schools, officials said.
The defence ministry said around 250 soldiers were dispatched on Friday to the city and nearby Keelung, which also reported landslides, to help clear roads and drain floodwater.
In Kaohsiung and neighbouring Pingtung, about 1,500 soldiers were deployed for a second day to aid in typhoon relief work, according to the defence ministry.
Taiwan is accustomed to frequent tropical storms from July to October, but scientists have warned climate change is increasing their intensity, leading to heavy rains, flash floods and strong gusts.
In July, Gaemi became the strongest typhoon to make landfall in Taiwan in eight years, killing at least 10 people, injuring hundreds and triggering widespread flooding in Kaohsiung.
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