Japan's Meteorological Agency uses an alert scale of one to five for situations caused by heavy rain.
It says a level 5 emergency alert applies to the kind of torrential downpour that occurs only once in several decades.
A level 5 alert also means there is a strong possibility that a disaster has already occurred. Residents should do whatever they can to protect themselves.
The other levels range from advisories about heavy rain up to evacuation orders.
The agency introduced the alert system in 2013.
It says residents should evacuate before a situation escalates to a level 5 alert, because there is a very strong probability that mudslides and flooding have already occurred by the time the warning is issued.