Among the 9 victims, three passed away while trapped within their flooded semi-basement residence, known as a banjiha, based on the ministry.
Local reports state the victims had been a teenager, her mom and her aunt.
Another sufferer died while removing a tree that had fallen onto a sidewalk, and is believed to have been electrocuted.
Another passed away after a landslide hidden his home within the mountainous Gangwon Province.
President Yoon, who on Wednesday visited the banjiha apartment, acknowledged Southern Koreans have “suffered a lot of damage”.
At a separate authorities meeting, he informed officials to pay work to the most vulnerable.
“Those who else struggle financially or with physical issues are bound to become more vulnerable to natural unfortunate occurances, ” he said.
The gathered rainfall in Seoul since midnight Monday stood at 525mm as of 7am upon Wednesday, according to the Korea Meteorological Administration (KMA), with more forecast. In neighbouring Yangpyeong Region, total rainfall hit 532. 5mm.
The KMA desires rain to continue in many parts of the country, with especially heavier rain within Chungcheong Province. The particular agency predicted that rainfall would gradually subside in many parts of the greater Seoul region and Gangwon State.
The government and the ruling People Energy Party are expected to hold an emergency meeting to discuss fiscal support regarding damage recovery.