Typhoon Nanmadol is bringing three times the average September rainfall to Japan in one weekend as it powers through the mainland towards Tokyo on Tuesday.
135mph winds are expected to strike the southernmost region Kagoshima late on Sunday with 40 centimetres of rain falling over 24 hours.
More than 9,000 people took shelter at evacuation centres in Kagoshima as the storm reached the coast, while a further 4,700 evacuated in neighbouring Miyazaki.
The region's power company said that close to 100,00 homes across Kyushu were without electricity after power lines were damaged.
Local government have issued their highest possible level five alert to the 14,000 people most at risk in Kagoshima, while sending evacuation orders to nearly two million.
Moving slowly towards Tokyo on Tuesday, the Japan Meteorological Agency has warned of flooding and landslides due to the volume of rainfall.
Visiting family in the Japanese capital, Damian Tingle, from West Yorkshire told ITV News: "We've been told to prepare for the worst of it on Tuesday. There is a warning in place."
The UK government have updated their travel advice for the country asking visitors to monitor Japanese weather forecasts.
The 14th typhoon of the season is expected to leave the Japanese mainland and head out to see on Wednesday.
Hundreds of domestic flights have been canceled with more potentially cut over the next couple of days. Bullet trains on Kyushu island have also been suspended.
Convenience store chain Seven-Eleven has temporarily closed around 950 shops as the storm passes.