The rampage exploded on Tuesday following a demonstration by thousands of Muslims protesting the alleged slaying of up to 600 of its adherents by Christian mobs last week in Yelwa.
"The Kano situation is an unfortunate development and just a reverberation of what happened in Yelwa," said Remi Oyo, spokeswoman for President Olusegun Obasanjo.
Obasanjo, ordered security agencies on Wednesday to "put a permanent end" to the violence, Oyo said.
Witnesses said mobs brandishing machetes and clubs went on a rampage, setting fires to buildings, and in one case "necklacing" a victims -- where a tire is thrown around a victims shoulders and set alight.
Late Wednesday, the ancient city was relatively quiet, the newspaper said.