Following two days of riots across the country at least ten people have died.
Protesters were angry at the cartoon on the front cover of the French Charlie Hebdo magazine.
It published the image a week after the terror attacks in Paris.
Initially it was thought around 40 churches had been hit in the violence.
Reports now suggest more than 200 Christian families are being housed in military camps amid fears of more protests.
The army says the homes of Christians have been identified and secured.
"The situation is currently extremely unstable despite assurances from the authorities," said an anti-persecution charity in Niger.
"Churches have not been placed under police protection despite assurances from the Ministry of Security yesterday...We are really scared."
Large-scale protests have also taken place in Pakistan, the Philippines, and Chechnya.
Twelve people who were working at the Paris offices of the Charlie Hebdo magazine were killed by two masked gunmen on 7 January and the magazine then went on to publish a cartoon of Muhammad on the front cover of its next issue on 13 January.