Police spokesman Haz Iwendi said 15 people were killed by rioters in the north-eastern state of Borno where the churches were burnt.
One one person died in similar riots in the north-central state of Katsina.
"The army is assisting the police and a curfew has been imposed," Iwendi said in reference to the Borno riot.
The Nigerian violence followed Friday's clashes in Libya, in which police killed 11 demonstrators protesting against the "provocative and outrageous" anti-Islamic insults of Italy's Reform Minister Roberto Calderoli.
Italian Prime Minister Silvio Berlusconi forced Calderoli to resign for provoking the clashes in Libya by wearing T-shirts lampooning the Prophet Mohammed.
Berlusconi said he hoped the resignation would "avoid acts of retaliation against our businesses and against our soldiers abroad".