The Central Weather Administration (CWA) lifted its typhoon warning early Friday as the storm slowly dissipated after slamming into the island the day before, bringing mudslides, flooding and destructive winds.
Across the island, two people were killed, one was missing and nearly 700 were reported injured, with more than 70,000 homes still without power as of Friday afternoon.
In the coastal city of Kaohsiung, where schools and offices remained closed, workers raced to clear away trees and fallen advertising signs that still blocked many streets and a light rail track.
"I think that there will need to be a lot of tough clean-up work to be done," a Kaohsiung resident surnamed Chan told AFP Thursday night.
"This disaster in Kaohsiung is quite severe."
More than 1,000 soldiers have been deployed to assist in clean-up efforts in the seaport city, the defence ministry said.
President Lai Ching-te on Friday thanked troops for their help and reminded the public to avoid going to the mountains or seaside as heavy rain continued in some areas.
"The central government will also fully assist local governments and provide all kinds of support. We will work together to restore our homes as soon as possible," he said in a Facebook post.
Kaohsiung mayor Chen Chi-mai said his city government was "making every effort" to repair the typhoon damage.
Wind speeds of 56.3 metres per second, or 203 kilometres (126 miles) per hour, were measured in Kaohsiung on Thursday, according to the CWA.
Krathon uprooted trees, blew cargo containers off a pier, and shattered the glass doors of businesses across the city.
Local TV footage showed convenience store workers trying to brace a glass door before it was shattered by strong gusts, sending goods flying inside the shop.
The typhoon also disrupted water supplies in nearly 130,000 homes across Kaohsiung until Friday around noon.
In southern Pingtung, which also remained shuttered, the typhoon hampered rescue efforts when a fire tore through a hospital, killing nine people on Thursday.
Torrential rain also lashed northern Taiwan during the typhoon, triggering landslides in New Taipei City and Keelung, where about a dozen garbage trucks and other vehicles were buried in mud on Friday after a slope collapsed near an incinerator facility where they were parked, local media reported.
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.
bur-aw/smw
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