Interior Ministry officials told The New York Times at least six Christians and five Muslims died and about 220 people were wounded, including 65 shot by bullets, in hours of fighting that lasted until 4 a.m.
Ministry spokesman Alla Mahmoud said the violence reportedly was set off Saturday evening by reports that a Christian woman married to a Muslim was being held in the St. Mena Coptic Orthodox Church against her will, CNN reported.
Soon after the church was attacked, another nearby Coptic church was set on fire, witnesses told the broadcaster.
The country's military used the social networking Facebook site to announce the prosecution of demonstrators, the BBC said.
"The Supreme Military Council decided to send all those who were arrested in yesterday's events, that is 190 people, to the Supreme Military Court," the military said in Sunday's posting.
The clashes renewed a streak of violence that started with 23 people killed in a New Year's Day bombing of a Coptic church in Alexandria.
The EgyNews agency said Prime Minister Essam Sharaf postponed a trip to Bahrain and the United Arab Emirates to keep abreast of the religious violence.
Coptic Christians number about 10 percent of Egypt's predominantly Muslim population.