The "massacre ...Started in March and then assumed dramatic proportions" mainly in island settlements on the Niger river, the prefect of the Ayorou region, Jando Rhichi Algaher, told AFP.
Large numbers of hippos and several bird species have made Ayorou, about 200 kilometres from the capital Niamey, a popular place for tourists.
Patrols by troops "have helped slow the slaughter", Algaher said.
"The locals have killed a large number of hippopotamuses, although this species is protected," Environment Minister Almoustapha Garba said on state radio.
Tension is high in Ayorou after the arrest of about ten people suspected of killing a hippopotamus. Some of the suspects have been freed, Algaher said.
In May, local tribal chiefs issued warnings about hippos, saying they were ravaging crops and threatening boats on the Niger river.
In 2014, 12 schoolchildren aged between 12 and 13 were killed when a hippo attacked their boat on the Niger at Libore, a village near Niamey.
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