The train, carrying around 250 passengers, was hit by the mudslides as it was approaching a tunnel in Pingtung county, the Taiwan Railway Administration said, adding that four carriages came off the tracks. [break]
Three people were seriously hurt while nine others suffered minor injuries. The injured were treated in hospital.
The rest of the passengers were later put on another train and repair work is under way.
Tropical Storm Kong-Rey pounded Taiwan on Thursday, leading to widespread flooding in the south that left three people dead and caused more than $11 million in agricultural damage, the government said.
Floodwaters rose to a depth of three metres and the storm disrupted air and rail traffic, forcing offices and schools to close.
Television footage showed rescuers in rubber boats helping evacuate people while cars were stranded on submerged roads.
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