The protesters torched at least eight houses of worship in Niamey on Saturday. Bars, hotels and various businesses under non-Muslim ownership or bearing signs of French companies were also targeted.
It was the second day of violence in the west African country over the Mohammed cartoon, after five people were killed and 45 injured in protests in Niger's second city of Zinder on Friday.
By Saturday evening calm had returned to Niamey, where police were stationed outside the city's cathedral and other religious buildings, the AFP correspondent said.
"In Niamey, the tally is five dead, all civilians," Niger's President Mahamadou Issoufou said in a speech broadcast on state television, appealing for calm.
He added the death toll in Zinder had climbed from four to five after a body was found "burned inside a church".
"Those who loot these places of worship, who desecrate them and kill their Christian compatriots ... have understood nothing of Islam," he said.
French Foreign Minister Laurent Fabius, whose country has defended the Charlie Hebdo cover as freedom of expression, also condemned "the use of violence, today in Niamey and yesterday in Zinder".
Around 255 Christians were placed under military protection in Zinder on Saturday, sheltered in barracks, a Western security source said. Another 70 had sought refuge in an evangelical church protected by police, two of the Christians there told AFP.
Muslim elder Yaou Sonna, speaking on behalf of around 20 of his peers, called for restraint, saying on state television: "Don't forget that Islam is against violence. I urge men and women, boys and girls to calm down."
Earlier in the day around 100 helmeted riot police stood in front of the Niamey cathedral to protect it from a crowd of stone-throwing youths.
Police used tear gas to disperse another crowd of about 1,000 young people massed in front of Niamey's grand mosque who were armed with iron bars and clubs.
"They burned everything after smashing anything that was glass on the road," said Kiema Soumaila, manager of the Toulousain, a well-known bar in Niamey.
France's embassy in its poverty-stricken former colony warned French citizens to stay indoors after rioters ransacked several French-linked businesses, including telephone kiosks run by Orange.
The satirical weekly Charlie Hebdo has repeatedly published cartoons of Mohammed over the years and its latest issue, released on Wednesday, features a cartoon of Mohammed on its cover holding a Je Suis Charlie (I Am Charlie) sign under the headline "All Is Forgiven".
It was published a week after attacks by three Islamists on the weekly's offices, a kosher supermarket and a policewoman left 17 people dead in Paris over three days, deeply shocking the country and sparking an outpouring of international support.
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