They said police were trying to control the situation. There was no immediate report of any injuries or fatalities.
The sources said earlier local residents pelted the pro-Morsi demonstrators with rocks as they marched on the country's Ministry of Religious Endowment.
Protests in Egypt have continued since the nation's military removed Morsi from office.
Two of Morsi's top aides were arrested Tuesday, officials said.
Cairo prosecutor Misr el-Gedida ordered the detention of Ahmed Abdel Ati, who managed Morsi's office, and Ayman Hodhod, an adviser to the deposed president, Ahram Online reported. The two are being investigated for the alleged involvement in clashes between Morsi supporters and opponents outside the presidential palace in Cairo in December, the website said.
Egyptian Judge Hassan Samir Monday extended Morsi's detention for an additional 15 days pending an investigation of his alleged collaboration with Hamas, the website said.
Since his July 3 ouster, Morsi along with a number of his top aides, have been held at an undisclosed location.
Morsi is accused of collaborating with Hamas to facilitate his escape from a prison during the 2011 violence that led to the ouster of former President Hosni Mubarak. Morsi is also charged with attacking police stations with intent to kill and of espionage, the website said.