The holy buildings were destroyed during angry protests by Muslims unhappy at the depiction shown in the most recent edition of Charlie Hebdo magazine.
Five people have died and 130 others injured in the demonstrations which have mainly taken place in the capital Niamey.
Charlie Hebdo put the cartoon on its front cover after an Islamist attack on its offices in Paris that took 12 people's lives.
Protesters initially took to the streets in the former French colony after Friday prayers and reporters on the scene say some are also angry at the government.
45 churches were set on fire in #Niger during #CharlieHebdo protests http://t.co/yTD4xVrg0S pic.twitter.com/GSX6UJG1rs
— Sputnik (@SputnikInt) January 19, 2015Amadou Abdoul Ouahab, who took part in the demonstration, told Reuters: "They offended our Prophet Mohammad, that's what we didn't like.
"This is the reason why we have asked Muslims to come, so that we can explain this to them, but the state refused. That's why we're angry today."
Police fired tear gas at the gangs who were throwing petrol bombs and stones in retaliation, some held posters saying they were 'Kouchi', in reference to the name of one of the Paris attackers.
The protests had been banned by the government.
Elsewhere peaceful demonstrations took place in Mali, Senegal, Mauritania, Algeria and Pakistan.
BREAKING: Two churches burnt down in Niger at anti-#CharlieHebdo protest - reports http://t.co/3Jsosc7yl3 pic.twitter.com/ghcEMPNRWl
— RT (@RT_com) January 17, 2015