They were accused of taking part in acts of violence in Assiut last year during which five churches, several police stations and a number of shops were set on fire. There were no reported casualties.
The court acquitted 61 others standing trial in the same case, the source said.
Violent clashes erupted across Egypt on August 14, 2013, as news spread across the country of a violent dispersal by the police and army of two protest camps in Cairo set up by Morsi supporters.
Dozens of churches and church properties were attacked across Egypt after the bloodshed, in response to perceived Coptic Christian support for Morsi's ouster.
The crackdown since then has left at least 1,400 people dead and more than 15,000 imprisoned.
The ex-president and many top leaders of his now-banned Muslim Brotherhood are themselves in jail and on trial in cases in which they face the death penalty if convicted.
Dozens of Morsi supporters have been sentenced to death after mass trials which the United Nations says are "unprecedented" in recent history.
