Dozens of angry protesters have attacked the French cultural centre and three churches in Niger's second biggest city in response to France's satirical magazine Charlie Hebdo's latest Prophet Muhammad cartoon, the head of the centre has said.

At least four people, including a policeman and three civilians, were killed and 45 injured in the unrest on Friday, the AFP news agency reported, citing the country's Interior Minister Massaoudou Hassoumi.

Kaoumi Bawa told AFP that a crowd of about 50 people smashed the French centre's entrance door in Zinder city on Friday and set fire to the cafeteria, library and offices in spite of warning shots fired by two police guards.

A Catholic church and two Protestant churches were ransacked, authorities in Zinder, which is in the south of the country near the border with Nigeria, said.

"We've never seen that in living memory in Zinder," an administration official said. "It's a black Friday."

Amadou Mamane, a journalist in Zinder, described "a human wave took out its anger on the streets of Zinder to protest against the caricature of Mohammed. They were mostly youths."