In Japan, typhoon season generally last between June and October. An average of 20 typhoons strike Japan each year, of various scale and intensity.
Typhoons are law pressure systems that form in the oceans in the Intertropical Convergence Zone. They cause rain outpours and gusts of wind during a few hours. Japanese people don’t fear much this frequent phenomenon as they are used to it and Japanese infrastructures are adapted to the sometimes erratic weather conditions of the country.
If a typhoon is announced before your departure to Japan, cancelling your travel is not necessary, as even in the case your flight is cancelled due to the weather conditions, it is still possible to take another plane the next day.
Typhoons last less than one day. During this period, it is not recommended to stay outside; however it is possible to enjoy indoor activities like visiting museums or going shopping in malls while waiting for the weather to improve. Clear sky and shiny weather always follow a typhoon.
Typhoon season should not prevent you from enjoying your holidays, as they are not a major limitation during a stay. Moreover, September is one of the cheapest and the most pleasant season to visit Japan, so why not trying it?