According to the 30 year normals (1981-2010) by Japan Meteorological Agency, the average yearly temperatures for central Tokyo is 16.3 degrees C, for Sapporo-city in Hokkaido is 8.9 degrees C, and for Naha-city in Okinawa is 23.1 degrees C. The weather averages are good indicators of what to expect any month. Please refer to the Monthly Mean and Monthly Total Tables by Japan Meteorological Agency.
Japan's rainy season typically begins in early May in Okinawa. In other regions, it usually runs from early June through around mid July. Also, August to October is the peak typhoon season in Japan. It's important to check the weather often during the season. Please refer to weather warnings and typhoon statistics (Japanese site) by Japan Meteorological Agency.
According to the Japan Meteorological Agency, there are 108 active volcanoes in Japan. Please be aware of volcanic warnings and restrictions when you visit any volcanic areas in Japan.