Jonathan imposed a curfew and appealed for an end to the violence that began when some rioters alleged ballot rigging during last weekend's presidential election, the BBC reported.
Red Cross volunteers said they treated 368 people injured in Monday's post-election clashes and that some people had died. However, details about the deaths weren't available.
"There were deaths but we concentrated on the injured," Umar Marigar, the Red Cross's national disaster coordinator, told the BBC.
Jonathan's chief rival, Gen. Muhammadu Buhari, who is from the north, told the BBC the violence was sad and unwarranted, and he disassociated himself and his party from the clashes.
"In the last 24 hours, there has been a spate of violence in the country. This has included the burning of churches and is a sad, unfortunate and totally unwarranted development," Buhari said in a statement. "I must emphasize that what is happening is not ethnic, religious or regional."
Jonathan, who is from southern Nigeria, was declared winner of Saturday's presidential election. The country's electoral commission said the incumbent received about 57 percent of the vote with 22.5 million votes to Buhari's 12.2 million votes.
International observers said the election was reasonably free and fair.
In Kaduna, television stations reported the house of Jonathan's running mate, Vice President Namadi Sambo, was set on fire Monday and shots were heard into Tuesday morning.
Jonathan had been vice president and took over when President Umaru Yar'Adua died last year.
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