The Brave Blossoms have trained despite flooded practice facilities that saw them wade through knee-deep water to get to the practice field.
Video of the team preparing for their Rugby World Cup clash with Scotland tomorrow in Yokohama, which may be cancelled, showed players walking down some stairs and wading through the water.
Some of the team got lifts over the water on the backs of their teammates while others tried to tiptoe around the water.
Tokyo and surrounding regions have already been hit hard by heavy rain.
According to the local news one person has died in the region of Chiba just outside of Tokyo city.
A cancellation of the Japan-Scotland match would end Scotland's tournament and secure the host nation a berth in their first-ever Rugby World Cup quarter-final.
Typhoon Higibis is the 19th storm to hit the region this year and is expected to bring record rainfall, with 500mm predicted to fall in Tokyo over a 24 hour period.