Ninjas were mercenaries in feudal Japan. In Ninja Hattori-kun they are from only two regions: the Koga and Iga regions.
The Iga Clan lives in a village for Iga-Ninjas. Some notable former residents are Hattori, Shinzo, Shishimaru and Tsubame. The Iga Region is a peaceful, non-violent dwelling and a lot of Ninja Academies have been found there. The weather is normal and has a temperate wind. Iga Tribes mostly eat fried eggs or drink just water during their training; younger Ninjas help the village elders. When a Ninja becomes an adult and become stronger, they are inducted into the Iga-Ninja order, and sometimes try to create their own Ninja techniques. Their civilisation started with a river called the Iga Aqua.
The Koga Clan is the more ruthless, competitive tribe, and they often challenge each other to fights. They live in a grassy area, and they take water from a very long river nearby the place called the Sacred Water of Koga, which began their civilisation. They once went to war with the Iga for stealing their sacred Ninja Technique scrolls. Koga Clan also has a known anthropomorphic animal in Kagechiyo.
The Karo Region is a tribe destroyed and conquered by the Koga Tribe. They were peace-loving and learnt Ninja techniques for competitions, not war. They were only shown in one of Hattori's flashbacks in the manga.
The Meso Clan may not have had the best of physical abilities, but they were wise and kind. Their land was very resourceful so the Koga Tribe conquered it. They were only shown in one of Hattori's flashbacks in the manga.