More than 40 people have lost their lives in less than a week of heavy rains - including 14 who died when floodwater trapped them in an underpass in the city of Cheongju.
The events have cast doubt on the country's efforts to prepare for more regular and intense downpours.
"Climate change is causing extreme natural disasters," Yoon told a Cabinet meeting televised live on Tuesday.
"We cannot respond to this unprecedented abnormal weather the way we have been doing until now."
He urged officials to mobilise all available resources for restoration work, calling the current situation an "emergency".
The disaster unfolded after downpours pummelled the country's central and southern regions since Thursday as the rainy season that started in late June reached its peak.
Fourteen deaths occurred in a tunnel in the central city of Cheongju, where 16 vehicles, including a bus, were swamped by a flash flood on Saturday after a river levee collapsed.
The government last year vowed to take steps to better cope with climate change-induced disasters after the heaviest downpours in 115 years pounded Seoul, including the glitzy district of Gangnam, leaving at least 14 dead and flooding subways, roads and homes.
The Korea Meteorological Administration has forecast more rain through to Wednesday. It warned that the weather conditions pose a "grave" danger.
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