The protesters torched at least eight houses of worship in Niamey. Bars, hotels and various businesses under non-Muslim ownership or bearing signs of French companies were also targeted, an AFP correspondent reported.
It was the second day of violence in the west African country, after five people were killed and 45 injured in protests in Niger's second city of Zinder on Friday.
"Some of us stayed barricaded in our homes. I have never been so scared in my life," a Christian mechanic in the capital told AFP.
By yesterday evening calm had returned to Niamey, where police were stationed outside the city's cathedral and other religious buildings.
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"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 that 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.
Around 255 Christians were placed under military protection in Zinder yesterday, sheltered in barracks, a Western security source said.
Another 70 had sought refuge in an evangelical church protected by police.
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.
"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.