Isahaya (諫早市 Isahaya-shi?) Isahaya is a growing town located in Nagasaki prefecture just a little northeast of Nagasaki city. It is about a 30-40 minute train ride away. It has a population of approximately 145,000 people. It is the hub for many train routes since it is located in an area that is connected to neighboring peninsulas. Isahaya is surrounded my many mountains and there is a river called Honmyo river which runs through the city..