Two of the three civilians were shot by police during an attack on their station, the agency quotes Interior Minister Hassoumi Massaoudou as saying on state television.
A police officer was run over and killed and 45 people were injured as police clashed with a crowd that attacked a French cultural center and set churches ablaze.
"Zinder experienced a quasi-insurrectional situation, a spontaneous protest of a criminal nature," the interior minister said. "I would like to reassure Christians that the state is here to defend those living in Niger at all costs."
The protests erupted after French satirical magazine Charlie Hebdo published more cartoon images of the Prophet Mohammad.
The demonstrators set French flags ablaze and attacked Christian shops with clubs and Molotov cocktails. Police responded with tear gas.
"The protesters were crying out in the local Hausa language: 'Charlie is Satan — let hell engulf those supporting Charlie'," Reuters quoted one of the witnesses, shopkeeper Aboubacar Mamane as saying.
Protests also erupted in Pakistan and Algeria, resulting in several injuries.
Peaceful marches took place after Friday prayers in the capital cities of several former French colonies in western Africa: Mali, Senegal and Mauritania.