A car drives past a fallen tree as Typhoon Krathon nears Kaohsiung, October 3. AFP-Yonhap

Southern Taiwan worked on Friday to clear up damage from flooding and high winds after Typhoon Krathon slammed into a major metropolis, while most of the rest of the island resumed work and financial markets re-opened.

Krathon, now downgraded to a tropical depression, made landfall in the port city of Kaohsiung, inundating streets with water, blowing out windows in some buildings and sending debris flying as record-breaking winds hit.

While the rest of Taiwan resumed work on Friday, local governments in Kaohsiung and neighbouring Pingtung county declared another day off work to remove downed trees, pump out floodwaters and remove detritus from roads.

Kaohsiung Mayor Chen Chi-mai, writing on his Facebook page, said some parts of the city got more rain than during the last storm, Typhoon Gaemi, in July.

"Given the long duration of the storm, coupled with the strong winds and heavy rain, the city government is doing its best to repair the damage," he wrote.

A man picks up fallen store signs after Typhoon Krathon made landfall in Kaohsiung, Taiwan, Oct. 3. Reuters-Yonhap

Tsai Ming-an, a 51-year old engineer, was cleaning up his house after flooding of about 20 cm (7.8 inches) came into his entire house on the ground floor.

"I have never seen winds like that. It was so bad," Tsai said.

Power remained down on Friday for 100,000 households, almost all in Kaohsiung and Pingtung.

The fire department said the death toll remained at two, both men killed on the mountainous east coast before the typhoon made landfall, with one person missing and 667 injuries.

Taiwan's north-south high speed rail line re-opened, as did most ordinary rail routes apart from two branch lines, though there was continued air transport disruption, with 13 international and 85 domestic flights cancelled.

At Kaohsiung port, some freight containers were blown off their stacks and workers were clearing them to ensure operations went unaffected, the transport ministry said.

Kaohsiung airport suffered damage to two air bridges, while the airport on the outlying Orchid Island had landing aids washed away, though both facilities remained open, the ministry added.

The government also said it was investigating the cause of a Pingtung hospital fire that broke out as the typhoon was bearing down, killing nine people. (Reuters)