Seo Jeong-il, head of the west Cheongju fire station, said an estimated 15 vehicles, including a bus, were submerged in the underpass in the city shortly after a levee of a nearby river was destroyed by the downpours on Saturday.
A dashcam video showed muddy water rushing into the tunnel as a driver manages to exit the underpass, while other CCTV footage aired on local broadcaster MBC showed vehicles driving past the tunnel with their wheels submerged.
The death toll in the tunnel stands at nine, including one body retrieved on Saturday, he said.
Kong Seong-pyo, a 60-year-old Cheongju resident who frequently uses the underpass, said the government should have restricted access to the tunnel when flooding was expected.
"I would have also died if I were submerged. I have no words to express this frustrating feeling," Kong told Reuters.
The Ministry of Interior and Safety said nine people were missing across the country as heavy downpours caused landslides and floods, with evacuation orders covering 8,852 people.
The ministry data does not include those in the flooded tunnel because it was not immediately clear how many people were trapped underwater.
The latest disaster took place despite South Korea's vow to step up preparedness against torrential rains after Seoul was hit last year with floods caused by the heaviest downpours in 115 years, inundating basement flats in low-lying neighbourhoods, including in the largely affluent Gangnam district.
A North Chungcheong province official said the levee unexpectedly collapsed before the precipitation reached the level required for restricting access to the tunnel.
President Yoon Suk Yeol, now on an overseas trip, convened a video-linked response meeting and said some regions had failed to take pre-emptive measures against the extreme weather.
Yoon ordered Prime Minister Han Duck-soo to mobilise all available resources to minimise casualties and urged the weather agency to quickly release forecasts because more heavy rain was expected in the coming days, his office said.
The Korea Meteorological Administration said the central and southern parts of the country could receive as much as 300mm of additional rain by Tuesday.
While South Korea often experiences heavy rains in summer, it has witnessed a sharp increase in torrential rains in recent years.
Korea Railroad Corp has halted all slow trains and some bullet trains since Saturday due to safety concerns over landslides, track flooding and falling rocks.
