Demonstrators were angry after the satirical magazine published the cartoon following the attacks in Paris.
Tear gas had to be fired in Niger's second city of Zinder as hundreds of people burned French flags on Friday, according to Reuters.
The Churches were attacked after Friday prayers at mosques around the city.
At least four people have died although it's not thought they were in the churches attacked.
Police officer homes and the French cultural centre were also looted and burnt in the former French colony.
Elsewhere peaceful protests took place in Mali, Senegal and Mauritania.
Last week the president of Niger marched alongside world leaders and more than a million French people in solidarity with the victims of the Paris attacks.