June in Nagasaki is the rainiest and the cloudiest month of the year. In June, the weather in Nagasaki is typically warm. Average daily high temperature in June is about 23 degrees above zero. On average, Nagasaki has 26 rainy, 2 sunny, and 2 cloudy days in June. The rains are usually heavy. June as well as January, February, July, and August is considered the most uncomfortable time to visit Nagasaki.