Hundreds of protesters attacked and burned two churches in the city of Sukkur, some 300 miles north of Karachi, in Sindh province, Channel NewsAsia reported. A school at one of the churches was also damaged, but no injuries were reported.
News reports suggested that a teenage boy started the trouble by throwing pages of the Muslim holy book into a trash can.
Protesters burned tires to block roads, leading to paramilitary troops being called in.
Police arrested 50 people, including the Christian, and managed to disperse a mob that attacked the police station, demanding the accused young man.
Police said the act of desecration may have been an attempt by the Christian to frame his father-in-law for blasphemy, a crime punishable by death in Pakistan.
The incident followed almost daily protests in the city over cartoons of the Prophet Mohammed published recently in European newspapers.