Nine million people have been told to leave their homes as one of the worst typhoons in the country's history wreaks havoc.
Two people have been killed by the super typhoon.
It hit Kyushu, the southernmost of Japan's four main islands, on Sunday morning and is on its way to Honshu.
Tens of thousands of people spent Sunday night in emergency shelters.
The country is bracing for a lot of flooding and slides.
Some areas were forecast to get up to 16 inches of rain in a single day.
Hundreds of flights and trains have been canceled. Sandbags have been put in place to protect some properties after many shops and businesses closed due to the weather.
On the southern tip of Japan's most southerly island, Kyushu, the typhoon hit on Sunday morning.
There is a river in Kyushu.
NHK reported that one man died when his car was submerged in flooding and another died after being buried in a slide. 87 people have been injured and one is still missing.
There are roofs ripped off buildings and billboards that have fallen over.
The storm is expected to pass over the main island of Honshu before heading out to sea. Heavy rain has caused the Tozai underground line to be suspended.
A level five alert, the highest on Japan's warning scale, has been issued for more than half a million people.
Nine million people have been told to leave parts of the Kyushu, Shikoku and Chugoku regions.
A super typhoon is defined as a storm with sustained wind speeds of at least 200 km/h. It's the same as a category four or five storm.
The Prime Minister delayed his visit to New York to monitor the impact of the storm.
A natural phenomenon known as La Nia has scientists predicting a very active Hurricane season.
Climate change may cause warmer sea surface temperatures in the Atlantic and Caribbean.
According to the Intergovernmental Panel on Climate Change, tropical storms will likely increase.
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