Prime Minister Yoshihide Suga has called for an emergency meeting to discuss the disaster.
A video clip posted on social media showed the moment that raging water swept through Atami, destroying several homes along its path as several frightened onlookers ran for their lives.
In the video, a woman was also heard saying, “that’s scary” just seconds before the flash flood hit.
The report said that police and firefighters are searching for the missing, as officials from Shizuoka asked for help from the national government to help in the emergency situation.
Railway operation near the site of the disaster has been suspended as rescuers and other emergency staff scour the area for survivors.
According to NHK, record heavy rains have been reported in Shizuoka as well as Kanagawa Prefecture in the last 48 hours, prompting local authorities to raise their alert about possible flooding and “sediment-related disasters”.
At least one person was reported injured in Kanagawa after a landslide caused a vehicle to overturn.
According to the Japanese meteorological agency, rains are expected to continue in several areas of Japan in the next two days.
Around the same time last year, at least 50 people were reported killed after heavy floods and landslides devastated southwestern Japan.